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Recent Replies
Answer: Kallisto and Salmon give different results
by
i.sudbery
14k
Back when they were first released, Kallisto and Salmon used much more similar algorithms, but those algorithms have diverged over time. In…
Comment: DESeq2 after GSVA "some values in assay are negative"
by
ATpoint
60k
What does GSVA has to do with DESeq2? The former is to test for gene sets, the latter for differential genes. GSVA is not an input for DESe…
Comment: sliding windows over genome
by
gubrins
▴
220
Thanks for your answer! Is this method going to work with a non-model genome assembly? Not sure if my genome is as available as the human g…
Comment: NCBI tblastx remote
by
GenoMax
115k
`tblastx` is an intensive search. If you are trying to do this against entire set of viral sequences then it is likely not going to work on…
Comment: How to count mapping rates for ChIP-seq?
by
Istvan Albert
93k
for example with samtools you would need to filter out unmapped (4), supplementary (2048) and secondary alignments (256) like so
samto…
Comment: Gene starts with "LOC" prefix ?
by
GenoMax
115k
Since `LOC` genes are uncharacterized there is likely no way to do GO enrichment analysis on those.
Comment: sliding windows over genome
by
gubrins
▴
220
I would like to have a file with the last sliding windows being the size of all the genome.
Comment: sliding windows over genome
by
gubrins
▴
220
that's at the chromosome level, I want a file with 1 as the first position of the first chromosome and the last position being the total le…
Comment: Conda http error
by
GenoMax
115k
Do you have a public IP address for your windows machine or not? You may be doing double NAT (if you have a private IP address).
Comment: Kallisto and Salmon give different results
by
mailard
•
0
Do you mean this one: --fr-stranded and --rf-stranded? I do cor test and correlation was less then 0.60
Comment: Compare two sequences in python
by
Debut
▴
20
I didn't understand the line "return comparison". Where does comparison come from?
Comment: Compare two sequences in python
by
Debut
▴
20
Thank you for your reply,
No matter in pandas or pure python. But the goal is to have two lists with the sequences to be able to access an…
Answer: Retrieving ensembl protein length with biomart
by
Ben_Ensembl
★
2.0k
Hi iatz,
You can't retrieve protein length directly from BioMart. However, you can retrieve the CDS length and divide by 3.
version 2.3.6
version 2.3.6