4

pybedtools assumes that bedtools is in your path and bedtools itself will return the version with bedtools --version. So: import subprocess subprocess.check_output(['bedtools', '--version'], text=True).strip().split()[1] For me that returns 'v2.30.0'.


2

I usually take into account library strandness during the mapping to the reference step (but I never worked with bigwig files myself). Assuming RNA-seq data from Illumina, you can use Hisat2 for alignment to the reference genome, and you have the option --rna-strandness to specify the strand-specificity information (default unstranded). This is ...


2

If your aligner has a strandedness option then go ahead and use it. The general idea here being that you'll preferentially align correctly to genes. Whether to bother with strandedness here depends on your goal. Are you interested in anti-sense transcription? Do you need to use the bigWig track to accurately quantify translational pausing or some other ...


1

It's not so much that you have "intronic contamination" or "genomic contamination", rather you're not selecting explicitly for full-length mature transcripts with rRNA depletion. That is the most common cause for higher intronic read rates. There's nothing you can do about this post-hoc, just continue along. BTW, many lncRNA's are ...


1

Strandedness should be taken into account at the mapping stage. If you are presented with only a BAM file, ask for the raw reads. If that's not possible, you can recover the reads (as fastq sequences) from the BAM file and/or remap them, but that conversion requires a lot more effort (e.g. most mappers expect the fastq files from each end to be sorted by ...


1

Firstly, right at the start if the experiment it's important that your RNA samples are processed with a strand-specific protocol (e.g. Illumina's TruSeq Stranded) in order to produce stranded libraries for sequencing. If the samples haven't been treated as such, then there's nothing you can do to correct it. Secondly, I'm not sure stranded protocols are ...


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