How to run peak calling only?
Closed this issue · 6 comments
I have computed alignments of deduplicated reads already and I want to input them for peak-calling. I am not sure how to best do this. What format is .db for database tag in 'clipseqtools' application? Is there a way to use bam/bed files as input?
clipseqtools all
--database proteinA/reads.adtrim.star_Aligned.out.single.sorted.collapsed.db
--gtf data/hg19/annotation/UCSC_gene_parts_genename.gtf
--rname_sizes data/hg19/chrom.sizes
--o_prefix clip/proteinA/
--plot
-v
Assuming that you have the .db file from a previous step you can use
clipseqtools cluster_size_and_score_distribution
--database proteinA/reads.adtrim.star_Aligned.out.single.sorted.collapsed.db
--o_prefix clip/proteinA/
--plot
-v
How do you get to the .db file? Is there a utility tool for converting bed/bam files to that? (I have deduplicated alignments in bam format)
clipseqtools-preprocess sam_to_sqlite.
fyi if you just execute each of the clipseqtools-preprocess, clipseqtools and clipseqtools-compare it will list the available commands and a short description.
Assuming that you have the .db file from a previous step you can use
clipseqtools cluster_size_and_score_distribution --database proteinA/reads.adtrim.star_Aligned.out.single.sorted.collapsed.db --o_prefix clip/proteinA/ --plot -v
I was able to use this command successfully but the output given were cluster_score_distribution and cluster_size_distribution files. In terms of peak-calling, I was wondering if there was any other subcommand that gave output as a list of peaks in bed/bam/sam files. I went through the list of available commands for 'clipseqtools' but I wasnt able to see an option like that.
I released a new version 1.0.0. In this new version, the above command will also output a BED file with the clusters coordinates. Could you please update to the latest version from CPAN and test?
Sorry for the late reply. Yes, it outputs the needed files. Thank you so much for your help.