Some regions are not loaded warning

[Amy Houseman]

Hello,

I received this warning from my results: 98 regions were skipped because chromosome name was not found in the BAM file.

Is there a reason behind this? 

Originally my bed file was lifted from hg19 to hg38, and then the chromosome ID was changed from UCSC to RefSeq (due to the bam and bed file not having the same IDs).

Any ideas? Or is this normal?

Thanks,

Amy

[Konstantin Okonechnikov]

Hi,

This warning reason is that certain annotated chromosome segments were not found to be present in the BAM file. This could be either if the alignment procedure was performed to the reference without these segments, or if there are some mixes/discrepancies in names of chromosomes in the BED file. The reference names present in the BAM file are listed in the "Chromosome stats" of the Summary segment in BAM QC report, so they could be inspected and compared to chromosome names that were noted as not found. 

Hope this helps,

   Konstantin

--
You received this message because you are subscribed to the Google Groups "QualiMap" group.
To unsubscribe from this group and stop receiving emails from it, send an email to qualimap+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/qualimap/8eff8ca4-7ef0-484a-88b2-ba1995df7e03n%40googlegroups.com.

[Amy Houseman]

Hi Konstantin, 

That does help. My qualimap pdf is attached, as well as the bed file used. I can't really understand why there would be regions not in the bam, this is the reference sequence I used was the GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

Thank you!

Amy

To view this discussion on the web visit https://groups.google.com/d/msgid/qualimap/CAMe83jn3rAWR_trQJ-xWkxKOSe4z-skqYWb6%3D21JRk4hJS8RfA%40mail.gmail.com.

[Konstantin Okonechnikov]

Hi Amy,

sorry, but where is the BED file? I do not see it attached. How did you create it? The issue was exactly because some regions sequence IDs stated in the annotation file were not found in the BAM file.

Best,

    Konstantin  

[Amy Houseman]

Hi Konstantinos, 

I reran my analysis and it turned out fine, I think some of my reads went missing when fastp ran so I reran with cutadapt & qualimap worked fine after that! 

Thanks for your help!

Amy

Get Outlook for iOS

---

From: qual...@googlegroups.com <qual...@googlegroups.com> on behalf of Konstantin Okonechnikov <k.okone...@gmail.com>
Sent: Monday, August 8, 2022 3:58:37 PM
To: qual...@googlegroups.com <qual...@googlegroups.com>
Subject: Re: Some regions are not loaded warning

 

--

You received this message because you are subscribed to the Google Groups "QualiMap" group.
To unsubscribe from this group and stop receiving emails from it, send an email to qualimap+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/qualimap/CAMe83jkArc_XLOD01UfWgaNT0SC71rC2m4HLGipgHuCsjCULLw%40mail.gmail.com.