Name: C_lusitaniae_DHED1_RNAseq
Owner: Jason Stajich Lab at UC Riverside
Description: C. lusitaniae DHED1 run 1
Created: 2017-12-15 19:37:11.0
Updated: 2018-05-11 20:57:47.0
Pushed: 2018-05-11 21:10:30.0
Homepage: null
Size: 74250
Language: R
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RNAseq for Candida (Clavispora) lusitaniae project from Deborah Hogan / Elora Demers
Samples are listed in samples.txt
Read Mapping stats are in mapping_stats.tsv
Summary plots and data for RNASeq
StringTie Results - don't use but for comparison. Data file is DHED1.DESeq.gene_count.tab
GSNAP featureCount Fragments - also don't use but for comparison. Data file is DHED1.gsnap_frags.tab
GSNAP featureCount Reads - USE ME Data file is DHED1.gsnap_reads.tab
Kallisto counting and TPM. Jobs run from 07_kallisto.sh (arrayjob) after running 00_build_kallisto_index.sh
GSNAP Jobs are run as:
q 24 | parallel bash jobs/01_gsnap.sh {}
atch --array=1-24 jobs/01_gsnap.sh
q 24 | parallel bash jobs/02_make_bam_gsnap.sh {}
atch --array=1-24 jobs/02_make_bam_gsnap.sh
Earlier analyses used HISAT2 which reportedly would respect strand-specific nature of these RNAseq libraries, but apparently did not. So these were scrapped, but archived for comparison
jobs/00_build_index.sh SINGLE
jobs/01_hisat2.sh - map the reads - run with array jobs or using parallel SLURMARRAY
q 24 | parallel bash jobs/01_hisat2.sh {}
atch --array=1-24 jobs/01_hisat2.sh
jobs/02_make_bam.sh - run with array jobs or using parallel SLURMARRAY
q 24 | parallel bash jobs/02_make_bam.sh {}
atch --array=1-24 jobs/02_make_bam.sh
03_stringtie.sh - compute RNAseq expr SLURMARRAY
04_get_counts.sh - make count table for DEseq SINGLE
05_stats_pairedend.sh - summarize read-pair strandedness SLURMARRAY
Alternative pipline for GSNAP
See the Expression reports from these runs in reports