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Popular Question to
Wietje
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Friederike
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seta
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Recent Replies
Comment: Fasta file is not converting properly to Indexed Fasta File
by
dariober
13k
[U00096](https://www.ncbi.nlm.nih.gov/nuccore/U00096.3/) appears to be *E. coli* so one entry in the index file is ok. @Maliha: well behave…
Comment: What Is The Best Method To Find Orthologous Genes Of One Species And Compare Wit
by
Friederike
8.4k
I am not aware of a benchmark study that would allow me to pinpoint the best resource, but a very good one that I use frequently is <https:…
Comment: Why different read depth on IGV and in VCF for a variant
by
Friederike
8.4k
You'll have to re-sequence that locus. Or look at replicate samples that are expected to have the same variants.
Comment: Comparing two CUT&RUN (similar to ChipSeq) generated peaks
by
Friederike
8.4k
The HBC Training link gives most details you'll need.
The basic steps are:
1. obtain normalized *coverage* files of your CUT&RUN samples (…
Comment: Fasta file is not converting properly to Indexed Fasta File
by
Friederike
8.4k
Seconding this, you can also read a bit more about this [here](https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Referen…
Answer: Difference between clusterProfiler and gProfileR
by
ATpoint
64k
The basic principle is similar but each tool has their own way of defining background genes and calculating enrichment stats + multiple tes…
Answer: Fasta file is not converting properly to Indexed Fasta File
by
i.sudbery
15k
How many contigs do you have in your fasta file?
Samtools faidx doesn't convert a fasta file into an indexed fasta, it produced an inde…
Answer: Writing a fasta file in R
by
margo
▴
40
I have managed to solve my problems with the details in this link:
https://bootstrappers.umassmed.edu/guides/main/r_writeFasta.html
Answer: Comparing two CUT&RUN (similar to ChipSeq) generated peaks
by
babalyigit
▴
10
I am using this guideline for ChIPseq analysis. After the peak calling step by MACS2, this tutorial can be also used for CUT&RUN analysis. …
Answer: CWL and Arvados
by
Michael R. Crusoe
★
1.9k
There is a very good CWL plugin that pairs well with VS Code, called Rabix Benten. You can find a link to it and other CWL development aids…
Comment: CWL and Arvados
by
dariober
13k
I've never used CWL and Arvados. However, snakemake, which I use quite extensively, has the option to export a workflow as [CWL](https://sn…
Comment: phylip format sequence name/header issue
by
Michael Dondrup
52k
MrBayes will complain if the first 15 characters of the sequences do not lead to unique taxa though.
Answer: phylip format sequence name/header issue
by
Mensur Dlakic
★
20k
Phylip format can have an arbitrary number of characters in header, but not all the programs will tolerate it. MrBayes, for example, has no…
Answer: phylip format sequence name/header issue
by
Michael Dondrup
52k
I assume you have the sequences in a FASTA file. I recommend to shorten the sequences in FASTA format already, then convert to phylip forma…
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