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Recent Replies
Answer: Creating a local version of Clustered NR database
by
PeterC_NCBI
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260
Thanks @genomax
> This seems reasonable since it should capture significant part of sequence to search against ( 90% identity and 90% …
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
by
Pierre Lindenbaum
154k
1) read groups should have been specified from the start (eg. with bwa mem -R )
2) if you do'nt specify SORT_ORDER, the order is the same …
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
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100
Does it support substitution matrices - e.g. blossum62 - for local protein alignments ?
Does it support different gaps for gat open, and …
Comment: ChatGPT optimized for bioinformatics questions
by
Alexander
▴
100
May be you can consider to make a talk about that work for your community "sciBerloga" - see previous talks: https://www.youtube.com/@SciBe…
Answer: where to obtain hg19 reference transcriptome in gencode
by
GenoMax
130k
[**On this page**][1]
Transcriptome: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/GRCh37_mapping/gencode.v43lift…
Comment: GSEA application not launching
by
GenoMax
130k
If you have not, look in "System settings" and "security" to see if the OS is blocking the application from launching.
Comment: Decoding MM and ML tags in .SAM file
by
Alex Reynolds
35k
I made changes to how I decode m6A events and updated links in the answer above. Python code is in a separate repository. Javascript code i…
Comment: How do I calculate differential expression for RNA-seq values with the "limma" p
by
John
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0
So the manual uses CPM instead of TPM. Do I need to adjust the formulae they use, or is it still the same?
Also, in the manual, it uses a …
Answer: synteny viewer
by
cmdcolin
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3.0k
I compile a large list of visualization tools, here are all tools I have tagged "comparative" which can include synteny viewers https://cmd…
Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
Thank you for your kind comments.
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴
360
hi Jesse - we're hoping to build custom lab specific private experiences for folks. You can check it out here and reach out if you're inter…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
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360
This is awesome prodding. Will definitely try to address this use case; especially it being more explicit with the citations back to papers…
Answer: ChatGPT optimized for bioinformatics questions
by
Alexander
▴
100
Thanks for sharing !
I asked about score calculation answer is quite good , though the last example seems not fully correct
version 2.3.6
version 2.3.6