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Are there mm39/GRCm39 blacklist regions?
Comment: Can I successfully go from a bed file (narrowpeak) back to a bam file containing
Comment: Can I successfully go from a bed file (narrowpeak) back to a bam file containing
Answer: Retrieving ensembl protein length with biomart
Conda http error
Answer: Conda http error
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Back when they were first released, Kallisto and Salmon used much more similar algorithms, but those algorithms have diverged over time. In…
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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…
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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…
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`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…
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for example with samtools you would need to filter out unmapped (4), supplementary (2048) and secondary alignments (256) like so samto…
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Since `LOC` genes are uncharacterized there is likely no way to do GO enrichment analysis on those.
Comment: sliding windows over genome
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I would like to have a file with the last sliding windows being the size of all the genome.
Comment: sliding windows over genome
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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…
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Did you manage to solve that?
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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
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mailard
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Do you mean this one: --fr-stranded and --rf-stranded? I do cor test and correlation was less then 0.60
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I didn't understand the line "return comparison". Where does comparison come from?
Comment: Compare two sequences in python
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Debut
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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
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Hi iatz, You can't retrieve protein length directly from BioMart. However, you can retrieve the CDS length and divide by 3. ![enter image…
Comment: NCBI tblastx remote
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ailton
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I also tried doing Tblastx locally on my machine with the following command **$ makeblastdb -in reference.fasta -title reference -dbtype …
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