Question: PureCN: Estimating tumor purity and ploidy
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gravatar for sruthi
8 months ago by
sruthi20
sruthi20 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

TIA

sequencing next-gen • 227 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by sruthi20

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

ADD REPLYlink written 8 months ago by markus.riester480

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

Thanks Markus

ADD REPLYlink written 8 months ago by sruthi20

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 8 months ago by sruthi20

No idea, I would ask their support.

ADD REPLYlink written 8 months ago by markus.riester480
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