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4 votes
Accepted

How do I quantify a specific somatic variant?

I have a little function that can report this by using samtools to look at the read pileup. Um. It isn't the most elegant piece of code, but it does sorta do the job: ...
terdon's user avatar
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3 votes
Accepted

Can index hopping lead to more reads in samples?

The current best way to mitigate the effects of "index hopping" for short reads is to use dual / unique barcodes on each end of a sequenced library for each sample (as it appears you have ...
gringer's user avatar
  • 14.4k
3 votes

paired-end short reads: will one file suffice?

I suspect you won't be able to avoid assembling or aligning. If you are working with strains that don't have their own, well studied reference genome and so want to avoid aligning so as not to bias ...
terdon's user avatar
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2 votes

short Read/percentage threshold for bacterium presence in metagenome

Given that you're already using kraken2, I recommend bracken: https://github.com/jenniferlu717/Bracken Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies ...
gringer's user avatar
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2 votes
Accepted

short Read/percentage threshold for bacterium presence in metagenome

Thats an interesting question. I do this stuff all the time and don't have a fixed cut-off. What I am certain about is 100 is marginal evidence of a species. So I personally would be reluctant to ...
M__'s user avatar
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2 votes
Accepted

Where to obtain fastq_illumina_filter

I found this site after Googling fastq_illumina_filter and comparing the file name to that shown in an archived version of your link: https://www.sigenae.org/drap/...
Ram RS's user avatar
  • 2,425
2 votes

cellranger-arc throws an error when demultiplexing

I have found the solution to my problem. The only thing missing from the command I used was the instruction to regard the run as a ATAC/GEX step. This is done by adding the parameter ...
Assa Yeroslaviz's user avatar
2 votes
Accepted

How to get cytoband and gene level copy number from genome wide SNP array copy number data?

To obtain cytoband and gene-level copy numbers from genome-wide SNP array copy number data, you might want to consider using the ASCAT tool, as it makes allele-specific copy number segment data and ...
BigMistake's user avatar
1 vote
Accepted

Hybrid assembly versus polishing for hifi and illumina reads

Usually, if you have HiFi reads, there is no way you can improve the assembly with short reads. Not just that they don't have higher quality, but they also map a lot worse. People sometimes use short ...
Kamil S Jaron's user avatar
1 vote

How to interpret a GenomeScope plot?

Based on the numbers shown above the plot, and the appearance of the curve, this looks like reads from a diploid genome approximately 113Mb in length that was sequenced at around 174X coverage.
gringer's user avatar
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1 vote

Trimmomatic QC report shows drop in the reads and presence of overrepresented sequences

Given that it's a NovaSeq, these are almost certainly "no signal" reads as a result of the two-colour chemistry and should probably be excluded (or at least ignored). A long polyG sequence ...
gringer's user avatar
  • 14.4k
1 vote

paired-end short reads: will one file suffice?

The problem with using single-end short reads is that they're often not long enough to uniquely match to a database (especially for highly-conserved genes, like the ribosomal RNAs). Whether or not ...
gringer's user avatar
  • 14.4k
1 vote

what percentage of the human genome is MAPQ=0?

You might want to check out this paper: Ebbert MTW, et al., Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. Genome Biol. 2019 May 20;20(1):97. ...
terdon's user avatar
  • 10.2k

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