Question: PureCN: Estimating tumor purity and ploidy
gravatar for sruthi
15 days ago by
sruthi0 wrote:

Hi, I tried calculating GC normalized coverage by giving .bam file and intervals.txt file as input and the following error showed up. I tried viewing the BAM file for the error, but file size being big, it ain't happening. What should I do to troubleshoot the error?

Error in .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file), : seqlevels(param) not in BAM header: seqlevels: ‘chrY’ file: /path/to/sample.bam index: /path/to/sample.bam


sequencing next-gen • 85 views
ADD COMMENTlink modified 7 days ago • written 15 days ago by sruthi0

Are the BAM files aligned to the same FASTA file that was used to generate the interval file?

ADD REPLYlink written 14 days ago by markus.riester320

No. I will align the BAM file again and then run the tool.

Thanks Markus

ADD REPLYlink written 7 days ago by sruthi0

Hey, I would also like to know whether IDT xgen provides hg38.bed file. While looking for .bed files on their website, I could find only the one for hg19 and not hg38. Could you please give me a clarity on this?

TIA Sruthi

ADD REPLYlink written 7 days ago by sruthi0

No idea, I would ask their support.

ADD REPLYlink written 7 days ago by markus.riester320
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