02.10-bismark-deduplication

1 Intro

1.1 Inputs

This notebook is a continuation of using Bismark (Krueger and Andrews 2011) to perform methylation analysis. Read alignments were run in 02.00-bismark-bowtie2-alignment.Rmd. This step will perform deduplication (Bismark manual) of the BAM files generated by alignment. Results will be summarized by MultiQC (Ewels et al. 2016).

Expects input BAM filenames formatted like (e.g.):

• CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.bam

1.2 Outputs

• *_dedup.sorted.bam: Deduplicated, sorted BAMs.

• *_dedup.sorted.bam.bai: Deduplicated, sorted BAM index file. Useful for IGV.

• *.deduplicated.bam: Deduplicated BAMs. These are not sorted.

• *.deduplication_report.txt: Individual summary reports for each deduplication process.

• multiqc_report.html: A summary report of the alignment results generated by MultiQC, in HTML format.

Due to the large file sizes of BAMS, these cannot be hosted in the ceasmallr GitHub repo. As such these files are available for download here:

• https://gannet.fish.washington.edu/gitrepos/ceasmallr/output/02.10-bismark-deduplication/

2 Create a Bash variables file

This allows usage of Bash variables across R Markdown chunks.

{
echo "#### Assign Variables ####"
echo ""

echo "# Data directories"
echo 'export repo_dir=/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr'
echo 'export output_dir_top=${repo_dir}/output/02.10-bismark-deduplication'
echo 'export alignment_dir="${repo_dir}/output/02.01-bismark-bowtie2-alignment-SLURM-array"'
echo ""


echo "# Paths to programs"
echo 'export programs_dir="/home/shared"'
echo 'export bismark_dir="${programs_dir}/Bismark-0.24.0"'
echo 'export bowtie2_dir="${programs_dir}/bowtie2-2.4.4-linux-x86_64"'
echo 'export multiqc="/home/sam/programs/mambaforge/bin/multiqc"'
echo 'export samtools_dir="${programs_dir}/samtools-1.12"'
echo ""

echo "# Set number of CPUs to use"
echo 'export threads=40'
echo ""

echo "# Filename patterns"
echo "export deduped_filename_pattern='_R1_001.fastp-trim*bismark_bt2_pe.deduplicated.bam'"


echo "# Print formatting"
echo 'export line="--------------------------------------------------------"'
echo ""
} > .bashvars

cat .bashvars

#### Assign Variables ####

# Data directories
export repo_dir=/home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr
export output_dir_top=${repo_dir}/output/02.10-bismark-deduplication
export alignment_dir="${repo_dir}/output/02.01-bismark-bowtie2-alignment-SLURM-array"

# Paths to programs
export programs_dir="/home/shared"
export bismark_dir="${programs_dir}/Bismark-0.24.0"
export bowtie2_dir="${programs_dir}/bowtie2-2.4.4-linux-x86_64"
export multiqc="/home/sam/programs/mambaforge/bin/multiqc"
export samtools_dir="${programs_dir}/samtools-1.12"

# Set number of CPUs to use
export threads=40

# Filename patterns
export deduped_filename_pattern='_R1_001.fastp-trim*bismark_bt2_pe.deduplicated.bam'
# Print formatting
export line="--------------------------------------------------------"

3 Deduplication

# Load bash variables into memory
source .bashvars

# Make output directory, if it doesn't exist
mkdir --parents "${output_dir_top}"

cd "${alignment_dir}"

for bam in *_bismark_bt2_pe.bam
do
  # Set stderr filename
  stderr_name=$(echo "${bam}" | awk -F"." '{print $1"."$2".deduplication.stderr"}')
  
  # Run deduplication
  ${bismark_dir}/deduplicate_bismark \
  --samtools_path ${samtools_dir} \
  --paired \
  --bam \
  --output_dir ${output_dir_top} \
  ${bam} \
  > ${output_dir_top}/${stderr_name} 2>&1
done

4 Sorting

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"


for bam in *deduplicated.bam
do
  sample=$(echo ${bam} | awk -F"_" '{print $1}')
  ${samtools_dir}/samtools sort \
  -@ "${threads}" \
  -o ${sample}_dedup.sorted.bam \
  ${bam}
done

4.1 Check file counts

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"
ls -1 *deduplicated.bam | wc -l
ls -1 *dedup.sorted.bam | wc -l

5 Indexing for Downstream Applications

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"
find *dedup.sorted.bam \
| xargs basename -s _dedup.sorted.bam \
| xargs -I{} ${samtools_dir}/samtools \
index {}_dedup.sorted.bam

6 Checksums

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"

for file in *; do
  if [ "${file}" != "checksums.md5" ]; then
    md5sum "${file}" >> checksums.md5
  fi
done

7 MultiQC

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"

${multiqc} .

8 List output files

# Load bash variables into memory
source .bashvars

cd "${output_dir_top}"

ls -lh

total 238G
-rw-r--r-- 1 sam sam  520M Nov 26 07:36 CF01-CM01-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  604K Nov 26 09:55 CF01-CM01-Zygote_dedup.sorted.bam.bai
-rw-rw-r-- 1 sam sam  3.3K Nov 26 09:55 CF01-CM01-Zygote_R1_001.fastp-trim.deduplication.stderr
-rw-r--r-- 1 sam sam  578M Nov 25 12:07 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   315 Nov 26 09:55 CF01-CM01-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam  4.9G Nov 26 07:39 CF01-CM02-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.5M Nov 26 09:55 CF01-CM02-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  6.7G Nov 25 12:25 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF01-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  2.3G Nov 26 07:41 CF02-CM02-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.1M Nov 26 09:55 CF02-CM02-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  2.9G Nov 25 12:32 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF02-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  3.0G Nov 26 07:42 CF03-CM03-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.2M Nov 26 09:55 CF03-CM03-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  3.8G Nov 25 12:42 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF03-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  3.6G Nov 26 07:44 CF03-CM04-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.3M Nov 26 09:55 CF03-CM04-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  5.1G Nov 25 12:57 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   311 Nov 26 09:55 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF03-CM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  4.5G Nov 26 07:46 CF03-CM05-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.5M Nov 26 09:55 CF03-CM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  6.0G Nov 25 13:13 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF03-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  3.3G Nov 26 07:48 CF04-CM04-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.3M Nov 26 09:55 CF04-CM04-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  4.3G Nov 25 13:24 CF04-CM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 CF04-CM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF04-CM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  5.9G Nov 26 07:53 CF05-CM02-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.6M Nov 26 09:55 CF05-CM02-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  8.4G Nov 25 13:47 CF05-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   311 Nov 26 09:55 CF05-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF05-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  3.9G Nov 26 07:55 CF05-CM05-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.4M Nov 26 09:55 CF05-CM05-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  5.1G Nov 25 14:01 CF05-CM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 CF05-CM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF05-CM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  3.7G Nov 26 07:57 CF06-CM01-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.4M Nov 26 09:55 CF06-CM01-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  4.7G Nov 25 14:13 CF06-CM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 CF06-CM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF06-CM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  2.9G Nov 26 07:58 CF06-CM02-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.2M Nov 26 09:55 CF06-CM02-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  3.6G Nov 25 14:23 CF06-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 CF06-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF06-CM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  2.3G Nov 26 07:59 CF07-CM02-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.1M Nov 26 09:55 CF07-CM02-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  2.8G Nov 25 14:30 CF07-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 CF07-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF07-CM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  2.4G Nov 26 08:00 CF08-CM03-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.1M Nov 26 09:55 CF08-CM03-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  3.0G Nov 25 14:38 CF08-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 CF08-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF08-CM03-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam   62M Nov 26 08:00 CF08-CM04-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.1M Nov 26 09:55 CF08-CM04-Larvae_dedup.sorted.bam.bai
-rw-rw-r-- 1 sam sam  3.3K Nov 26 09:55 CF08-CM04-Larvae_R1_001.fastp-trim.deduplication.stderr
-rw-r--r-- 1 sam sam   65M Nov 25 14:38 CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   312 Nov 26 09:55 CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam   54M Nov 26 08:00 CF08-CM05-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.1M Nov 26 09:55 CF08-CM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam   58M Nov 25 14:38 CF08-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   305 Nov 26 09:55 CF08-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 CF08-CM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-rw-r-- 1 sam sam   15K Nov 26 09:55 checksums.md5
-rw-r--r-- 1 sam sam  3.1G Nov 26 08:02 EF01-EM01-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.3M Nov 26 09:55 EF01-EM01-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  4.0G Nov 25 14:49 EF01-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 EF01-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF01-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  3.3G Nov 26 08:03 EF02-EM02-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.3M Nov 26 09:55 EF02-EM02-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  4.3G Nov 25 15:01 EF02-EM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 EF02-EM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF02-EM02-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  2.2G Nov 26 08:05 EF03-EM03-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam 1011K Nov 26 09:55 EF03-EM03-Zygote_dedup.sorted.bam.bai
-rw-rw-r-- 1 sam sam  3.3K Nov 26 09:55 EF03-EM03-Zygote_R1_001.fastp-trim.deduplication.stderr
-rw-r--r-- 1 sam sam  2.7G Nov 25 15:08 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   318 Nov 26 09:55 EF03-EM03-Zygote_R1_001.fastp-trim.REPAIRED_bismark_bt2_pe.deduplication_report.txt
-rw-r--r-- 1 sam sam  4.6G Nov 26 08:07 EF03-EM04-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.5M Nov 26 09:55 EF03-EM04-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  5.9G Nov 25 15:23 EF03-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 EF03-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF03-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  4.6G Nov 26 08:09 EF03-EM05-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.5M Nov 26 09:55 EF03-EM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  6.1G Nov 25 15:39 EF03-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 EF03-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF03-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  1.3G Nov 26 08:10 EF04-EM04-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  635K Nov 26 09:55 EF04-EM04-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  1.5G Nov 25 15:43 EF04-EM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   308 Nov 26 09:55 EF04-EM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF04-EM04-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  5.2G Nov 26 08:14 EF04-EM05-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.6M Nov 26 09:55 EF04-EM05-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  7.5G Nov 25 16:04 EF04-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   311 Nov 26 09:55 EF04-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF04-EM05-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  3.4G Nov 26 08:16 EF05-EM01-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.3M Nov 26 09:55 EF05-EM01-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  4.6G Nov 25 16:16 EF05-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 EF05-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF05-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  784M Nov 26 08:17 EF05-EM05-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  580K Nov 26 09:55 EF05-EM05-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  860M Nov 25 16:18 EF05-EM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   307 Nov 26 09:55 EF05-EM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF05-EM05-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  5.3G Nov 26 08:22 EF05-EM06-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.6M Nov 26 09:55 EF05-EM06-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  7.5G Nov 25 16:39 EF05-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   311 Nov 26 09:55 EF05-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF05-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  5.3G Nov 26 08:27 EF06-EM01-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.6M Nov 26 09:55 EF06-EM01-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  7.5G Nov 25 17:00 EF06-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 EF06-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF06-EM01-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  4.4G Nov 26 08:30 EF06-EM02-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.4M Nov 26 09:55 EF06-EM02-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  5.9G Nov 25 17:16 EF06-EM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 EF06-EM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF06-EM02-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  1.3G Nov 26 08:31 EF06-EM06-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  644K Nov 26 09:55 EF06-EM06-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  1.6G Nov 25 17:23 EF06-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   309 Nov 26 09:55 EF06-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF06-EM06-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  1.6G Nov 26 08:31 EF07-EM01-Zygote_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  824K Nov 26 09:55 EF07-EM01-Zygote_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  1.9G Nov 25 17:29 EF07-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 EF07-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF07-EM01-Zygote_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  4.1G Nov 26 08:34 EF07-EM03-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.4M Nov 26 09:55 EF07-EM03-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  5.8G Nov 25 17:45 EF07-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 EF07-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF07-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  4.6G Nov 26 08:37 EF08-EM03-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.5M Nov 26 09:55 EF08-EM03-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  6.7G Nov 25 18:03 EF08-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   311 Nov 26 09:55 EF08-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF08-EM03-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
-rw-r--r-- 1 sam sam  4.2G Nov 26 08:40 EF08-EM04-Larvae_dedup.sorted.bam
-rw-rw-r-- 1 sam sam  1.4M Nov 26 09:55 EF08-EM04-Larvae_dedup.sorted.bam.bai
-rw-r--r-- 1 sam sam  5.6G Nov 25 18:18 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplicated.bam
-rw-rw-r-- 1 sam sam   310 Nov 26 09:55 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication_report.txt
-rw-rw-r-- 1 sam sam  3.2K Nov 26 09:55 EF08-EM04-Larvae_R1_001.fastp-trim_bismark_bt2_pe.deduplication.stderr
drwxrwxr-x 2 sam sam  4.0K Nov 26 09:55 multiqc_data
-rw-rw-r-- 1 sam sam  1.1M Nov 26 09:55 multiqc_report.html

Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics 32 (19): 3047–48. https://doi.org/10.1093/bioinformatics/btw354.

Krueger, Felix, and Simon R. Andrews. 2011. “Bismark: A Flexible Aligner and Methylation Caller for Bisulfite-Seq Applications.” Bioinformatics 27 (11): 1571–72. https://doi.org/10.1093/bioinformatics/btr167.