Hi everyone, I am currently trying to run the command in DANPOS3 - which is a software to analyse nucleosome positions and call peaks. This is the command
$python3 danpos.py dpos <filename.bam> [optional parameters]
The bam file I am using was created using Galaxy. So the reads were aligned using Bowtie2 and then using "samtools view" I obtained only chromosome 5 reads. I validated this file for any errors using "Validatesamfiles" which assess SAM/BAM files, I was able to conclude that there are no errors.
However, after running the above the command, I get the following error
ERROR: empty BAM file
Is something wrong with the header file? It looks like this with the @SQ for all chromosomes
@HD VN:1.0 SO:coordinate @SQ SN:chr10 LN:129993255` @PG ID:bowtie2 PN:bowtie2 VN:188.8.131.52 CL:"/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-5bee08a20f60a5597c4ecd54735d608dc6a44caf6f433cd52f23c80aa5a38d02/bin/bowtie2-align-s --wrapper basic-0 -p 10 -x /cvmfs/data.galaxyproject.org/byhand/mm9/mm9full/bowtie2_index/mm9full -U input_f.fastq.gz"`
If there is no error in the BAM file when I validate, why would I get empty BAM file when I run the first mentioned command?? I am so new to this analysis of nucleosome positions, any insights into this will help!!
Thanks in advance