Comments (7)
We had a similar issue, adding a step of samtools fixmate
to BAM
processing fixed the insert sizes.
from methylseq.
We had a similar issue, adding a step of
samtools fixmate
toBAM
processing fixed the insert sizes.
Thank you I can try that!
from methylseq.
Yes, I've seen this before too. I'm pretty sure that the data is fine and it's an artefact from Qualimap. I have no idea why it happens - any ideas?
from methylseq.
Where does the Multqc stores the data from Qualimap? These numbers are normalized in Multiqc so I would like to see how normalization was calculated. Alternatively, the peak is a single pair from PE, (around 130bp) that appears clearly when data are normalized, so it end up in one narrow bin.
from methylseq.
The relevant code is here: https://github.com/ewels/MultiQC/blob/39d83c2e5991f8911e7f522987a1c8f5851c9c5b/multiqc/modules/qualimap/QM_BamQC.py#L158-L175
From memory (it was a long time ago), the Qualimap plot also shows the same spike though I think? So I didn't think it was down to the MultiQC parsing..
from methylseq.
See a similar repeat of this conversation on the nf-core Slack: https://nfcore.slack.com/archives/CP3RJSMF0/p1620159835062100
Our conclusion this evening is again that it's something weird in the Qualimap plotting, as it doesn't seem to be replicated by other tools. I don't think that it's MultiQC that is introducing the peak - the raw data from Qualimap seems to contain it too (see the Multi BamQC report plot). As such I'm not sure that there is much we can do except for ignoring the bump / pushing this upstream to the Qualimap developers.
from methylseq.
Hello again,
Some years later and this issue is still there. I can't replicate the peak with other software (like fastp), so it does look like a bug of the methylseq pipeline. Did you ever report this to the Qualimap developers in the end? I don't see an issue for that in their Github. Are you planning any solutions/updates (like maybe using alternative software to Qualimap)?
from methylseq.
Related Issues (20)
- Add CX report support from bismark_methylation_extractor HOT 7
- Add `asTair`
- Support for NuGEN Ovation RRBS HOT 2
- samplesheet input is not detecting entire values in sample column HOT 6
- Create metro map HOT 1
- Add gemBS option
- CG CHG and CHH with --comprehensive flag using bismark workflow HOT 8
- --rrbs and --emseq parameter and argument usage
- typo in samplesheet in README.md?
- Latest template merge completely broke dev branch (on AWS + Fusion) HOT 4
- Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency HOT 1
- Schematic for the methylseq pipeline
- bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided. HOT 2
- AS-XS tag missing
- Write tests for samplesheet sample merging/grouping
- Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option)
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- Multiple issues in the pipeline HOT 1
- samplesheet handling: different path + same filename gives an error
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from methylseq.