Hello everyone,
After Next Gen Sequencing, alignment (BWA), sorting and indexing (samtools), I obtained a bam file. I would like to know there is any tool allowing me to , when using a sliding windows on a bam file, discriminate fragments fully spanning the window from the other ones ?
For instance : To calculate a score for a given window, i would add +1 for each fragment completely spanning the window and -1 for the fragments having an endpoint in the window. Any Suggestions please ?
Thanks in advance.
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written
by
w.elmselmi •
I've quickly written the following tool: https://github.com/lindenb/jvarkit/wiki/Biostar234230
Not fully checked/tested.
See the code for more information about the reads that are included/discarded.
$ curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20110915_CEUtrio_b37_decoy_alignment/CEUTrio.HiSeq.WGS.b37_decoy.NA12892.clean.dedup.recal.bam" | java -jar dist/biostar234230.jar
#contig start end pairs_in_window pairs_over_window pairs_partial_overlap
1 10000 10100 0 2 240
1 10050 10150 4 615 274
1 10100 10200 0 800 276
1 10150 10250 0 216 649
1 10200 10300 0 2982 809
1 10250 10350 0 2918 207
1 10300 10400 0 1923 2851
1 10350 10450 0 227 4498
1 10400 10500 0 31 1971
(...)
Thank you Pierre !
Could you explain me how your script manages paired end reads ?
it ignores the following reads:
Ok Thanks. I'll try to make a python version, i'll keep you informed.
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what's the final aim of such tool ?
The aim is to infer nucleosomes locations