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Recent Replies
Comment: Convert amino acid sequences into nucleotide sequences
by
sperezilvia
▴
10
Look, I'm just preprocessing sequences. My boss, that did all the experimental data is checking everything, don't worry. They give me instr…
Comment: Convert amino acid sequences into nucleotide sequences
by
sperezilvia
▴
10
I tried without the -o parameter and I still got the same message as before and no sequences in the screen
Comment: Convert amino acid sequences into nucleotide sequences
by
sperezilvia
▴
10
The nucleotide fasta file is one of the output files of pRESTO (atleast2). But I can't do these things with pRESTO, I checked.
Comment: Match variants from RNAseq with known databases
by
dilokef367
•
0
Moving to vcfanno, which is more flexible. Thanks for your help.
Comment: Match variants from RNAseq with known databases
by
Ram
40k
I'm not sure that the default for the tool is - I always specify `-c none` explicitly because I want CHROM+POS+REF+ALT level uniques.
Comment: Match variants from RNAseq with known databases
by
dilokef367
•
0
The default is CHROM+POS+REF+ALT ? I'm looking here https://samtools.github.io/bcftools/bcftools.html#isec with no luck
Comment: Convert amino acid sequences into nucleotide sequences
by
Matthias Zepper
4.1k
If you are already working with pRESTO, why are you trying to come up with your own custom filtering instead of using [the tool that is par…
Answer: DEG gene list and find common TF from public ChlP-Seq data
by
Trivas
★
1.5k
I've used the R package `TFEA.ChIP` but it feels a little limited and hard to explain to a general biology audience.
Answer: GOSt Plot
by
Trivas
★
1.5k
A hacky solution would be to use `trace(gostplot, edit=TRUE)` and manually change the size of the points. Changes are temporary and not rep…
Comment: Convert amino acid sequences into nucleotide sequences
by
Joe
21k
But you say here you have a reference genome:
>Yes, there is a reference genome of the specie.
Comment: How can I compute energy from a protein PDB file?
by
Ram
40k
Cross-posted on bioinfo SE as well: https://bioinformatics.stackexchange.com/questions/21614/how-can-i-compute-energy-from-a-protein-pdb-fi…
Comment: Match variants from RNAseq with known databases
by
Ram
40k
Your concern is valid. bcftools has options to match CHROM & POS, CHROM+POS+REF and CHROM+POS+REF+ALT. You either need to ensure your varia…
Comment: Rna-seq analysis using FASTA file
by
Ram
40k
> to convert FASTA sequences for SARS CoV-2 from GISAID into read counts matrix
> after assigning dummy scores to my fasta file to convert…
Comment: Convert amino acid sequences into nucleotide sequences
by
sperezilvia
▴
10
Yeah, I know, thank you. Just please understand since I'm working with data not published I can't talk a lot about it.. I know what I have …
Comment: Convert amino acid sequences into nucleotide sequences
by
sperezilvia
▴
10
sorry, data analysis with pRESTO (Immcantation tool)
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