/volume2/web/Atumefaciens/20210908-cbai-hisat2-cbai_transcriptome_v3.1

RNAseq Alignments - C.bairdi Day 2 Infected-Uninfected Temperature Increase-Decrease RNAseq to cbai_transcriptome_v3.1.fasta with HISAT2 on Mox.

- 20210908-cbai-hisat2-cbai_transcriptome_v3.1.sh: SLURM script to run job on Mox HPC.

- <library_name>.sorted.bam: Sorted BAM alignment files for each library.

- <library_name>.sorted.bam.bai: BAM index file for each library. Useful for IGV.

- <library_name>_hisat2.err: HISAT2 standard error file. Contains alignment statistics.

- checksums.md5: MD5 checksums for all files in this directory.

- input_fastqs_checksums.md5: MD5 checksums for FastQ files used in alignments. Also serves as a list of FastQ files used.

- program_options.log: Log of program options/help menus used in SLURM script.

- slurm-2190600.out: Standard output captured by SLURM job.

- system_path.log: Log of system $PATH at runtime.

Notebook:

https://robertslab.github.io/sams-notebook/2021/09/08/RNAseq-Alignments-C.bairdi-Day-2-Infected-Uninfected-Temperature-Increase-Decrease-RNAseq-to-cbai_transcriptome_v3.1.fasta-with-Hisat2-on-Mox.html