Description: Use kallisto to quantify A. pulchra RNAseq transcript abundances
Inputs:
Trimmed RNAseq reads (e.g. *.fastq.gz). A. pulchra reads found here.
Transcripts FASTA (e.g. rna.fna) – note we are using transcripts from A. millepora, not A. pulchra. Downloaded from NCBI. Kallisto will also accept a gzipped reference fasta (e.g. *.fna.gz)
Outputs:
kalisto counts matrix (kallisto.isoform.counts.matrix)
This allows usage of Bash variables (e.g. paths to common directories) across R Markdown chunks.
{
echo "#### Assign Variables ####"
echo ""
echo "# Data directories"
echo 'export Apul_dir=/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul'
echo 'export output_dir_top=${Apul_dir}/output/14-Apul-RNAseq-kallisto'
echo 'export trimmed_reads_dir=${output_dir_top}/trimmed-reads'
echo 'export kallisto_output_dir=${output_dir_top}/kallisto'
echo ""
echo "# Input/Output files"
echo 'export Amil_ncbi_downloads_dir=${Apul_dir}/data/Amil'
echo 'export transcriptome_fasta_dir=${Amil_ncbi_downloads_dir}/ncbi_dataset/data/GCF_013753865.1'
echo 'export transcriptome_fasta_name="rna.fna"'
echo 'export transcriptome_fasta="${transcriptome_fasta_dir}/${transcriptome_fasta_name}"'
echo 'export kallisto_index_name="Amil_kallisto_index.idx"'
echo "# External data URLs"
echo 'export trimmed_reads_url="https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/"'
echo 'export transcriptome_fasta_url="https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_013753865.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCF_013753865.1.zip"'
echo ""
echo "# Set filename patterns"
echo "export ncbi_accession='GCF_013753865.1'"
echo "export fastq_pattern='*.fastq.gz'"
echo "export R1_fastq_pattern='*_R1.fastq.gz'"
echo "export R2_fastq_pattern='*_R2.fastq.gz'"
echo ""
echo "# Paths to programs"
echo 'export kallisto=/home/shared/kallisto_linux-v0.50.1/kallisto'
echo 'export trinity_abund_to_matrix=/home/shared/trinityrnaseq-v2.12.0/util/abundance_estimates_to_matrix.pl'
echo ""
echo "# Set number of CPUs to use"
echo 'export threads=20'
echo ""
echo "# Programs associative array"
echo "declare -A programs_array"
echo "programs_array=("
echo '[kallisto]="${kallisto}" \'
echo '[trinity_abund_to_matrix]="${trinity_abund_to_matrix}" \'
echo ")"
} > .bashvars
cat .bashvars#### Assign Variables ####
# Data directories
export Apul_dir=/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul
export output_dir_top=${Apul_dir}/output/14-Apul-RNAseq-kallisto
export trimmed_reads_dir=${output_dir_top}/trimmed-reads
export kallisto_output_dir=${output_dir_top}/kallisto
# Input/Output files
export Amil_ncbi_downloads_dir=${Apul_dir}/data/Amil
export transcriptome_fasta_dir=${Amil_ncbi_downloads_dir}/ncbi_dataset/data/GCF_013753865.1
export transcriptome_fasta_name="rna.fna"
export transcriptome_fasta="${transcriptome_fasta_dir}/${transcriptome_fasta_name}"
export kallisto_index_name="Amil_kallisto_index.idx"
# External data URLs
export trimmed_reads_url="https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/"
export transcriptome_fasta_url="https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_013753865.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCF_013753865.1.zip"
# Set filename patterns
export ncbi_accession='GCF_013753865.1'
export fastq_pattern='*.fastq.gz'
export R1_fastq_pattern='*_R1.fastq.gz'
export R2_fastq_pattern='*_R2.fastq.gz'
# Paths to programs
export kallisto=/home/shared/kallisto_linux-v0.50.1/kallisto
export trinity_abund_to_matrix=/home/shared/trinityrnaseq-v2.12.0/util/abundance_estimates_to_matrix.pl
# Set number of CPUs to use
export threads=20
# Programs associative array
declare -A programs_array
programs_array=(
[kallisto]="${kallisto}" \
[trinity_abund_to_matrix]="${trinity_abund_to_matrix}" \
)Reads are downloaded from: https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/
The --cut-dirs 4 command cuts the preceding directory structure (i.e. Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/) so that we just end up with the reads.
# Load bash variables into memory
source .bashvars
wget \
--directory-prefix ${trimmed_reads_dir} \
--recursive \
--no-check-certificate \
--continue \
--cut-dirs 4 \
--no-host-directories \
--no-parent \
--quiet \
--accept "RNA-*.fastq.gz" ${trimmed_reads_url}
ls -lh "${trimmed_reads_dir}"Already performed, can view multiqc report at https://gannet.fish.washington.edu/Atumefaciens/20230519-E5_coral-fastqc-fastp-multiqc-RNAseq/A_pulchra/trimmed/multiqc_report.html
# Load bash variables into memory
source .bashvars
# Download NCBI data zip file
curl \
-JX GET ${transcriptome_fasta_url} \
-H "Accept: application/zip" \
-o ${Amil_ncbi_downloads_dir}/${ncbi_accession}.zip
# Unzip
unzip ${Amil_ncbi_downloads_dir}/${ncbi_accession}.zip -d ${Amil_ncbi_downloads_dir}
# Delete the (now superfluous) zip file
rm ${Amil_ncbi_downloads_dir}/${ncbi_accession}.zip
ls -lh ${Amil_ncbi_downloads_dir}No checksum file(s) provided with ncbi download, so skippping this step
# Load bash variables into memory
source .bashvars
cd "${kallisto_output_dir}"
${programs_array[kallisto]} index \
--threads=${threads} \
--index="${kallisto_index_name}" \
"${transcriptome_fasta}"
ls -lh ${kallisto_output_dir}
[build] loading fasta file /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/rna.fna
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
from 49 target sequences
[build] warning: replaced 806 non-ACGUT characters in the input sequence
with pseudorandom nucleotides
KmerStream::KmerStream(): Start computing k-mer cardinality estimations (1/2)
KmerStream::KmerStream(): Start computing k-mer cardinality estimations (1/2)
KmerStream::KmerStream(): Finished
CompactedDBG::build(): Estimated number of k-mers occurring at least once: 63409924
CompactedDBG::build(): Estimated number of minimizer occurring at least once: 15547313
CompactedDBG::filter(): Processed 110666638 k-mers in 50570 reads
CompactedDBG::filter(): Found 63496221 unique k-mers
CompactedDBG::filter(): Number of blocks in Bloom filter is 433468
CompactedDBG::construct(): Extract approximate unitigs (1/2)
CompactedDBG::construct(): Extract approximate unitigs (2/2)
CompactedDBG::construct(): Closed all input files
CompactedDBG::construct(): Splitting unitigs (1/2)
CompactedDBG::construct(): Splitting unitigs (2/2)
CompactedDBG::construct(): Before split: 626678 unitigs
CompactedDBG::construct(): After split (1/1): 626678 unitigs
CompactedDBG::construct(): Unitigs split: 855
CompactedDBG::construct(): Unitigs deleted: 0
CompactedDBG::construct(): Joining unitigs
CompactedDBG::construct(): After join: 596827 unitigs
CompactedDBG::construct(): Joined 30174 unitigs
[build] building MPHF
[build] creating equivalence classes ...
[build] target de Bruijn graph has k-mer length 31 and minimizer length 23
[build] target de Bruijn graph has 596827 contigs and contains 63551545 k-mers
total 123M
-rw-r--r-- 1 shedurkin labmembers 118M Jan 31 16:21 Amil_kallisto_index.idx
-rw-r--r-- 1 shedurkin labmembers 2.0M Jan 31 16:19 kallisto.isoform.counts.matrix
-rw-r--r-- 1 shedurkin labmembers 0 Jan 31 16:19 kallisto.isoform.TMM.EXPR.matrix
-rw-r--r-- 1 shedurkin labmembers 2.4M Jan 31 16:19 kallisto.isoform.TPM.not_cross_norm
-rw-r--r-- 1 shedurkin labmembers 532 Jan 31 16:19 kallisto.isoform.TPM.not_cross_norm.runTMM.R
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:26 kallisto_quant_sample140
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:29 kallisto_quant_sample145
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:33 kallisto_quant_sample150
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:36 kallisto_quant_sample173
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:39 kallisto_quant_sample178Kallisto can run quantification on either single- or paired-end reads. The default option is paired-end, which requires the input of an even number of paired fastq files (e.g., pairA_R1.fastq, pairA_R2.fastq). To use single-end mode, include the –single flag, as well as -l (–fragment-length=DOUBLE, estimated avg. fragment length) and -s (–sd=DOUBLE, estimates stand. dev. of fragment length), and a number of fastq files. Again, gzipped files are acceptable.
Kallisto quant is rather finicky about how you input sets of paired reads, and you can only input a single pair at a time. To circumvent, I’ll create symlinks to each of the input files with simplified names, create a quantification function, and apply it iteratively to each pair using a loop.
# Load bash variables into memory
source .bashvars
# Create sym links to each of the trimmed read files with simplified names
for file in "${trimmed_reads_dir}"/*.fastp-trim.20230519.fastq.gz; do
# Extract sample ID and read number from the file name
sample_id=$(echo "$file" | grep -oP 'RNA-ACR-\K\d+')
read_number=$(echo "$file" | grep -oP '_R\K\d+')
# Create the shortened name
shortened_name="sample${sample_id}_R${read_number}.fastq.gz"
# Create symbolic link
ln -s "$file" "${trimmed_reads_dir}/${shortened_name}"
echo "Created link: ${shortened_name}"
done
ls -lh ${trimmed_reads_dir}ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample140_R1.fastq.gz': File exists
Created link: sample140_R1.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample140_R2.fastq.gz': File exists
Created link: sample140_R2.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample145_R1.fastq.gz': File exists
Created link: sample145_R1.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample145_R2.fastq.gz': File exists
Created link: sample145_R2.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample150_R1.fastq.gz': File exists
Created link: sample150_R1.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample150_R2.fastq.gz': File exists
Created link: sample150_R2.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample173_R1.fastq.gz': File exists
Created link: sample173_R1.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample173_R2.fastq.gz': File exists
Created link: sample173_R2.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample178_R1.fastq.gz': File exists
Created link: sample178_R1.fastq.gz
ln: failed to create symbolic link '/home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/sample178_R2.fastq.gz': File exists
Created link: sample178_R2.fastq.gz
total 27G
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 30 18:09 multiqc_data
-rw-r--r-- 1 shedurkin labmembers 2.9G May 19 2023 RNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 3.0G May 19 2023 RNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 2.6G May 19 2023 RNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 2.6G May 19 2023 RNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 2.6G May 19 2023 RNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 2.7G May 19 2023 RNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 2.9G May 19 2023 RNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 3.0G May 19 2023 RNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 2.6G May 19 2023 RNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
-rw-r--r-- 1 shedurkin labmembers 2.7G May 19 2023 RNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample140_R1.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-140-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample140_R2.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-140-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample145_R1.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-145-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample145_R2.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-145-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample150_R1.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-150-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample150_R2.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-150-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample173_R1.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-173-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample173_R2.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-173-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample178_R1.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-178-S1-TP2_R1_001.fastp-trim.20230519.fastq.gz
lrwxrwxrwx 1 shedurkin labmembers 150 Jan 25 11:46 sample178_R2.fastq.gz -> /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/trimmed-reads/RNA-ACR-178-S1-TP2_R2_001.fastp-trim.20230519.fastq.gz# Load bash variables into memory
source .bashvars
# Function to run kallisto quant. Takes two (paired) reads as input, outputs to sample-associated directory
run_kallisto_quant() {
source .bashvars # Source .bashvars inside the function to make its variables accessible
local R1_fastq=${1}
local R2_fastq=${2}
cd ${kallisto_output_dir}
sample_num=$(basename "${R1_fastq}" "_R1.fastq.gz")
mkdir kallisto_quant_${sample_num}
${programs_array[kallisto]} quant \
--threads=${threads} \
--index="${kallisto_output_dir}/${kallisto_index_name}" \
--output-dir="${kallisto_output_dir}/kallisto_quant_${sample_num}" \
--bootstrap-samples=100 \
${trimmed_reads_dir}/${R1_fastq} ${trimmed_reads_dir}/${R2_fastq}
}
# Iteratively apply run_kallisto_quant on each pair of input reads
for file_r1 in "${trimmed_reads_dir}"/*_R1.fastq.gz; do
# Extract the sample name from the file name
sample_name=$(basename "${file_r1}" "_R1.fastq.gz")
# Form the file names (function takes input file names, not paths)
file_r1_name="${sample_name}_R1.fastq.gz"
file_r2_name="${sample_name}_R2.fastq.gz"
# Check that the sample hasn't already been quantified
if [ ! -d "${kallisto_output_dir}/kallisto_quant_${sample_name}" ]; then
# Check if the corresponding R2 file exists
if [ -e "${trimmed_reads_dir}/${file_r2}" ]; then
# Run kallisto quant on the file pair
run_kallisto_quant "${file_r1_name}" "${file_r2_name}"
echo "Processed sample: ${sample_name}"
fi
else
echo "Sample already processed: ${sample_name}"
fi
done# Load bash variables into memory
source .bashvars
cd ${kallisto_output_dir}
${programs_array[trinity_abund_to_matrix]} \
--est_method 'kallisto' \
--gene_trans_map 'none' \
--out_prefix 'kallisto' \
--name_sample_by_basedir ${kallisto_output_dir}/kallisto_quant_*/abundance.tsv
ls -lh ${kallisto_output_dir}-reading file: /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/kallisto/kallisto_quant_sample140/abundance.tsv
-reading file: /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/kallisto/kallisto_quant_sample145/abundance.tsv
-reading file: /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/kallisto/kallisto_quant_sample150/abundance.tsv
-reading file: /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/kallisto/kallisto_quant_sample173/abundance.tsv
-reading file: /home/shared/8TB_HDD_02/shedurkin/deep-dive/D-Apul/output/14-Apul-RNAseq-kallisto/kallisto/kallisto_quant_sample178/abundance.tsv
* Outputting combined matrix.
/home/shared/trinityrnaseq-v2.12.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix kallisto.isoform.TPM.not_cross_norm > kallisto.isoform.TMM.EXPR.matrixCMD: R --no-save --no-restore --no-site-file --no-init-file -q < kallisto.isoform.TPM.not_cross_norm.runTMM.R 1>&2
sh: 1: R: not found
Error, cmd: R --no-save --no-restore --no-site-file --no-init-file -q < kallisto.isoform.TPM.not_cross_norm.runTMM.R 1>&2 died with ret (32512) at /home/shared/trinityrnaseq-v2.12.0/util/support_scripts/run_TMM_scale_matrix.pl line 105.
Error, CMD: /home/shared/trinityrnaseq-v2.12.0/util/support_scripts/run_TMM_scale_matrix.pl --matrix kallisto.isoform.TPM.not_cross_norm > kallisto.isoform.TMM.EXPR.matrix died with ret 6400 at /home/shared/trinityrnaseq-v2.12.0/util/abundance_estimates_to_matrix.pl line 385.
total 123M
-rw-r--r-- 1 shedurkin labmembers 118M Jan 31 16:21 Amil_kallisto_index.idx
-rw-r--r-- 1 shedurkin labmembers 2.0M Jan 31 16:21 kallisto.isoform.counts.matrix
-rw-r--r-- 1 shedurkin labmembers 0 Jan 31 16:21 kallisto.isoform.TMM.EXPR.matrix
-rw-r--r-- 1 shedurkin labmembers 2.4M Jan 31 16:21 kallisto.isoform.TPM.not_cross_norm
-rw-r--r-- 1 shedurkin labmembers 532 Jan 31 16:21 kallisto.isoform.TPM.not_cross_norm.runTMM.R
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:26 kallisto_quant_sample140
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:29 kallisto_quant_sample145
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:33 kallisto_quant_sample150
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:36 kallisto_quant_sample173
drwxr-xr-x 2 shedurkin labmembers 4.0K Jan 25 13:39 kallisto_quant_sample178