bowtie step about atacseq HOT 11 CLOSED

Another point, in align.sh, lines 63 and 72, I think that hg19.promoter.bed.gz should be remplaced by ${ATYPE}.promoter.bed.gz to permit mm10 use if indicated?

from atacseq.

Usually the FASTA file and the bowtie index are in the same directory. bowtie just expects the FASTA and then finds the corresponding index files automatically. Your 2nd point is fixed now, thanks for reporting.

from atacseq.

Thank you for your respone, I will try to put fasta file in bowtie index directory.

I think there is another typo in homer.sh line 28, hg19 should be remplaced by ${HG}?

Best,

from atacseq.

I think I replaced this already.

from atacseq.

Ok sorry I didn't see the commit.

However you replaced hg19 by ${ATYPE}, then you have to pass this in arguments in file atac.sh line 51?
Or can we indicate the fasta file to annotatePeaks.pl, in this case we could replace ${ATYPE} by ${HG}?

from atacseq.

That was too quick, sorry. I pass in now the analysis type.

from atacseq.

Thank you a lot for your fast response and updates!

Another point (the last I think): I have to run first
perl /home/marc/Programs/ATAC/tobiasrausch/bin/envs/atac2/share/homer-4.9.1-6/.//configureHomer.pl -install mm10
to run without error annotatePeaks.pl in homer.sh and findMotifsGenome.pl in motif.sh, otherwise I obtained an error message:
!!!!Genome mm10 not found in /home/marc/Programs/ATAC/tobiasrausch/bin/envs/atac2/share/homer-4.9.1-6/.//config.txt To check if is available, run "perl /home/marc/Programs/ATAC/tobiasrausch/bin/envs/atac2/share/homer-4.9.1-6/.//configureHomer.pl -list" If so, add it by typing "perl /home/marc/Programs/ATAC/tobiasrausch/bin/envs/atac2/share/homer-4.9.1-6/.//configureHomer.pl -install mm10"

Best,

from atacseq.

I think that's true. The Makefile should show how to do it for hg19.

from atacseq.

I have a last question. In footprint.sh, you have a if condition before alfred annotate line 54, restricting its execution to hg19.

Yet it seems that there are some murine transcription factors in ./motif/jaspar.gz, could we also run alfred annotate for mm10?

from atacseq.

To be honest, I never fully trusted this ATAC footprinting hypothesis. What makes sense in my opinion is to annotate the mm10 reference with murine transcription factor binding sites and then looking for overlaps with peaks and enrichment/depletion compared to a randomized background (shuffled peaks).

from atacseq.

ok thank you for all your responses.

from atacseq.