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nf-core / nascent

Nascent Transcription Processing Pipeline
https://nf-co.re/nascent
MIT License
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Flipped bigwig strands in PROseq samples #115

Open Caffeinated-Code opened 1 year ago

Caffeinated-Code commented 1 year ago

Description of the bug

Hi Edmund, I am raising a ticket here for the strand-flipping issue I mentioned on slack.

Bug: BigWigs generated for PROseq samples appear to be flipped. The strand carrying the gene body signal is inconsistent with gene direction. Example: GUSB gene on the negative strand. Genebody signal in the public Jurkat sample processed with the v2.1.1 pipeline is on the positive strand (UCSC Browser view attached). The same issue was observed in internal PROseq samples as well.

Command used and terminal output

nextflow run nf-core/nascent -profile docker --input /home/ec2-user/environment/sampleSheets/sampleSheet.public_Jurkat.202306.csv \
    --assay_type PROseq \
    --tracedir ./pipeline_info \
    --fasta /home/ec2-user/environment/annotations/bwa/hg38as.fa \
    --bwa_index /home/ec2-user/environment/annotations/bwa \
    --gtf /home/ec2-user/environment/annotations/gencode.v38.chr_patch_hapl_scaff.annotation.gtf 
    --filter_bed /home/ec2-user/environment/annotations/hg38as.blacklist.ENCODEDCC.bed \
    -w /data/work --outdir /data/outdir/public.Jurkat.GSE66031/ -resume > public.Jurkat.202306.log 2>&1

Relevant files

image

System information

Nextflow version: 23.04.1 Hardware : AWS Cloud9 Executor : Local Container engine : Docker OS: Nascent pipeline version: v2.1.1-g9ff33c7

edmundmiller commented 1 year ago

Sweet thanks, I was just about to make an issue for this!

These are the config pieces that control that https://github.com/nf-core/nascent/blob/9cba10b3970fff8483a7997ef6a028e47058430a/conf/modules.config#L110-L118

These look like the two relevant sections of the script linked, and it doesn't look like I got the -strand flipped or the naming... https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L868-L882 https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L1143-L1156

edmundmiller commented 1 year ago

Relevant sections for flipping proseq(@Caffeinated-Code): https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L829-L857 https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L863-L866