ngs-fzb / binosnp Goto Github PK

Hi there,

I'd like to use binoSNP to detect subpopulations in my eukaryotic RNA-seq data and tried to set it up accordingly by supplying my own list of intervals, mutation table and (multiple scaffold/chromosome) reference sequence.

Although binoSNP appears to run smoothly on the supplied files, the output is empty.
I'm currently don't know where the issue is but wondered if you could provide an example bam.file to test that binoSNP runs smoothly in my environment?

Also, I'd appreciate any tips on how to use binoSNP on eukaryotic data sets.

Many thanks in advance for your help!

I don't have system perl, mine is in a different location
This will ensure the first one in PATH is used.

http://www.github.de/ngs-fzb/binoSNP is in the paper

www.github.de's server IP address could not be found.

Hi, I have a problem when running the script, it does not detect the *.bam file. This is the terminal output:

./binoSNP ./GATK_Bam/*.bam

[2022-04-14 00:45:33] Processing ./GATK_Bam/sequence_01.gatk.bam

[2022-04-14 00:45:33] Starting bam-readcount

[2022-04-14 00:45:33] bam-readcount ./GATK_Bam/sequence_01.gatk.bam -b 20 -w 0 -f /home/.../binoSNP/var/M._tuberculosis_H37Rv_2015-11-13.fasta -l /home/.../binoSNP/var/Resisnps_Master.v28.interval_list.tsv > Low_Freq/sequence_01.gatk.txt
sh: 1: bam-readcount: not found

[2022-04-14 00:45:33] bam-readcount ./GATK_Bam/sequence_01.gatk.bam -b 20 -w 0 -f /home/.../binoSNP/var/M._tuberculosis_H37Rv_2015-11-13.fasta -l /home/.../binoSNP/var/Resisnps_Master.v28.interval_list.tsv > Low_Freq/sequence_01.gatk.txt did not work: 32512

What do you think is the problem?

best regards
Ricardo