leanq / splitreader Goto Github PK

It seems that reads in $BAMname-$TE-split-local-down.bam with more (LENGTH-20)/2 hard mapping should be contained in $BAMname-$TE-split-5+.bam.

(Take "SRR492382.16324611/1" for example)

So there are duplicate reads in $BAMname-$TE-up.bam which would influence the calculation of depth of $BAMname-$TE-up.bam. It will also influence the calculation of "($4+$8)>=rea "(depth of up.banm + depth of down.bam) when deciding the insertion of TE.

I used your test data, but I couldn't get the results in the last step.

code: bash SPLITREADER-beta1.2.sh -c SPLITREADER_configuration_file_example.txt

Error:
[E::hts_open_format] Failed to open file "/data1/home/mingzhang/SPLITREADER/SPLITREADER/Tmptest/QD-64848/results-64848/test-TE1.sam" : No such file or directory
samtools view: failed to open "/data1/home/mingzhang/SPLITREADER/SPLITREADER/Tmptest/QD-64848/results-64848/test-TE1.sam" for reading: No such file or directory

I'm pretty sure I wrote the right path of samtools.

I wonder if you could give me some advice.
Thanks a lot!
--Ming