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1500 questions
7
votes
4 answers
How do I rename fasta headers?
I am trying to use the seqkit replace command to replace chromosome names in the format chr_I, chr_II, ... to I, II, .... I am using the following command:
seqkit replace -p "(.)" --replacement "{kv}" --kv-file keyValues.txt mySequence.fasta
My…
Biomagician
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7
votes
1 answer
How can I speed up INDEL calling/correction on BAM files?
The samtools mpileup command has quite a neat feature that it is able to correct mapping errors associated with misalignment of INDELs. By default, the mpileup command will not work for reads that have more than 250X coverage of the reference…
gringer
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7
votes
2 answers
What is "Possible polymerase run-on fragment"?
I used gffcompare recently to compare a newly assembled transcriptome and a published transcriptome. The class code "p" transcripts are "possible polymerase run on".
What does that mean? I tried very hard but still cannot find the answer.
l0110
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7
votes
1 answer
Network comparison of single cells (from sequencing data)
What methods can we use to compare networks (PPI, gene regulatory etc) created from single-cell gene expression (or proteomics) data?
There are methods that construct networks by comparing two conditions (e.g. from (gene) co-expression, or…
Peter
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7
votes
3 answers
Finding the optimal resolution parameter in Seurat's FindClusters function
In Seurats' documentation for FindClusters() function it is written that for around 3000 cells the resolution parameter should be from 0.6 and up to 1.2. I am wondering then what should I use if I have 60 000 cells? How to determine that?
Nikita Vlasenko
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7
votes
3 answers
What is the difference between NGS, 2GS, SBS and HTS?
I've come across a bit of confusion about the initialism NGS, so think it would be a good idea to clarify this term (and similar terms like 2GS, SBS, and HTS) for this site with a bit of discussion.
What are the most common initialisms used to…
gringer
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7
votes
1 answer
FeaturePlot from Seurat: change its title
FeaturePlot is a function in Seurat package.
And in the vignette it is written that if we specify parameter do.return = TRUE it should return ggplot2 object. It is not working. My goal here is just to change the title of the plot. In case of violin…
Nikita Vlasenko
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7
votes
1 answer
Merge 2 VCFs from different variant callers
I am working with WES data for detection of somatic variants and I have used two variant callers because no variant caller is complete in itself. I have used GATK Haplotypecaller for small variants like snp,ins,del etc. And for large variants I have…
Lot_to_learn
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7
votes
3 answers
Merging sequencing data for ChIP-seq experiments
I need to merge sequencing data from different sequencing runs but for the same ChiP-seq library (HiSeq 2000).
Are there any potential advantages or disadvantages when merging files at .fastq or .BAM stage (alignment with Bowite/1.1.2)?
olga
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7
votes
3 answers
visualisation of genome alignment
I was asked to check the synteny of some genes in two genome assemblies of the same species (PacBio & Illumina). I was given two scaffolds couples (so 4 scaffolds total) in the Illumina genome and asked if they were assembled together in the PacBio…
aechchiki
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7
votes
1 answer
What's a template switching site?
Reading Islam et al. (2011):
From each transcript, a single read is obtained, corresponding to a template-switching site located preferentially at the 59 end of the mRNA.
By reading this page I think that a template switching site is an additional…
gc5
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7
votes
2 answers
How does htslib/samtools access optional BAM fields?
I am confused regarding how various software libraries deal with optional fields in a BAM:
Based upon the BAM specification, there are 11 mandatory fields to a BAM:
QNAME, FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN, SEQ, QUAL
The BAM files…
EB2127
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7
votes
4 answers
A good tool for gene locus visualization
Does anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to plug it into and get an image of the locus to…
Mgall
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7
votes
1 answer
Extracting strand specific reads from MinION cDNA-PCR protocol
I recently performed my first MinION run, and now I'm trying to analyze the data. Being pretty new to the bioinformatics field, I was hoping some of you could help me out.
As a bit of background, I'm trying to define transcript isoforms, and down…
Amy T
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7
votes
1 answer
Intuitive explanation of GSVA analysis
I'm trying to understand the way the GSVA analysis is working behind the scenes.And I was wondering if there is any way to understand it more intuitively the whole process.
So at first according to paper it starts by evaluating whether a gene i is…
J. Doe
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