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268

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Good mean coverage but big std in coverage

bamqc rnaseq qualimap coverage written 4 months ago by Pin.Bioinf • 210

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520

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Why difference in Hisat2 and bamqc from qualimap results?

bamqc qualimap rna-seq hisat2 written 9 months ago by Vasu • 270 • updated 9 months ago by Biostar ♦♦ 20

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understanding contig statistics

assembly mapping reads qualimap coverage spades written 23 months ago by mary • 0 • updated 23 months ago by Brian Bushnell ♦ 16k

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645

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Abnormal coverage profile

quality qualimap rna-seq rna degradation written 2.5 years ago by Gary • 450

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1.6k

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Qualimap result interpretation

qualimap written 4.1 years ago by Aura • 0 • updated 4.1 years ago by Antonio R. Franco • 3.9k

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Recent Replies

C: bedtools coverage gives error received illegal bin number, but that number isn't by Alex Reynolds ♦ 27k
You can also use `awk` to fix the input before running it through `bedops`: $ awk -vFS="\t" ...
C: Shotgun metagenomics: Why bother with de novo assembly? by jrj.healey ♦ 9.9k
16S still has its place for sure. You can’t beat it for cost. But, there’s no way around the abun...
A: bedtools coverage gives error received illegal bin number, but that number isn't by pangxy3 • 0
I got same error when using subtract of bedtools. And I have tried to use bedops to check one of...
C: Is it ok to use DREME to predict motifs from RNA-Seq data? by ytzhao • 0
Hello, I guess that you mean you now have several genes, in fasta format. you wanna find motif fr...
A: network with cytoscape by jpreethi569 • 0
Great information. I'm learning a lot from here. Do share more. https://www.fita.in/placement-tra...
C: How The Non-Canonical Intron Splice Sites Came Out? by ytzhao • 0
I appreciate your kind comment, but the url you gave was out of service now, would you like to se...
C: How to separate sequences of two species from Metagenomics Analysis? by shenwei356 ♦ 4.4k
Try mapping to E.coli first, check the coverage (they may share some genes), and assemble with un...
A: Parallel in PLINK for linear association for SNP effects by chrchang523 ♦ 4.3k
It’s plink 2.0, not 1.9, that has all the major optimizations for —linear. Using v2.0 for this s...
C: how to change the sequence ID and order of sequences in a file to match an align by finswimmer ♦ 8.9k
The desired output looks like it is just sorted sorted by sequence name. Shouldn't be `seqkit sor...
C: Finding 16 mer not present in GRCh38 by shenwei356 ♦ 4.4k
I found out 14-mers on my 48GB RAM PC, you can easily extend them to 16-mers. https://www.biosta...
C: Missing data in covariate file in PLINK by landscape95 • 150
Thank you very much! I have read this document but according to it, the --missing-phenotype will ...
A: Missing data in covariate file in PLINK by karl.stamm ♦ 3.4k
PLINK v1.9 has a parameter --missing-phenotype which lets you assign a number other than -9 as th...

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