search

wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
Other
49 stars 29 forks source link

count function start from external BAM file #81

Open jamesc99 opened 1 year ago

jamesc99 commented 1 year ago

Hi!

I want to inquire if I could only apply the Count function to RNA-seq BAM files instead of starting from the fastq files? I tried this on a BAM file downloaded from ENCODE and I got such error.

Thanks for your time and help!

Ryan

image image

Zha0rong commented 1 year ago

Hi!

I want to inquire if I could only apply the Count function to RNA-seq BAM files instead of starting from the fastq files? I tried this on a BAM file downloaded from ENCODE and I got such error.

Thanks for your time and help!

Ryan

image image

Hi @jamesc99 , I am also using the SQuIRE and met with this problem. From what I have observed it is probably due to the fact that the Count.py tries to read the header from bam file and infer whether the data is single-end or paired-end (line 311 in Count.py, function is_paired(bamfile,basename,tempfolder,debug)). One way to bypass this problem is to simply stop calling the is_paired() and directly set whether the data is paired-end or not. To do that, change: paired_end = is_paired(bamfile,basename,tempfolder,debug) to paired_end = True #is_paired(bamfile,basename,tempfolder,debug) or paired_end = False #is_paired(bamfile,basename,tempfolder,debug) Depending on what your data look like.