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Recent Replies
Comment: Mapping a predicted sequence to a genome
by
Mensur Dlakic
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23k
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome
by
Andy
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Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
Answer: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★
23k
If we are talking about organisms without introns, it is very simple. A tool to use is `tblastn` which can be accessed from the [**main BLA…
Comment: How to get information about promoter from bulk-RNAseq?
by
rfran010
▴
170
I'll just add what I did with my own dataset of ribo depleted RNA-seq:
I took predicted enhancer-promoter interaction datasets from UCSC a…
Answer: How to get information about promoter from bulk-RNAseq?
by
rfran010
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170
What type of RNA-seq data do you have?
With polyA, I think it will be hard to incorporate enhancer info without additional datasets.
…
Comment: Help with running ATAC using Encode pipeline
by
rfran010
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170
Yes, it is a lot to take in.
In your input json, is "atac.fastqs_wt_rep2_R2" valid?
This key should match exactly what is given in the exa…
Comment: How to calculate TPM from featureCounts output
by
rfran010
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170
Yes, I thought the featureCounts file is your counts file.
Comment: Limma returned only positive logFC values
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Gordon Smyth
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The code should be:
```
library(edgeR)
group<- factor(type)
design <- model.matrix(~group)
mrna.dge <- DGEList(counts=mat, group=group)
ke…
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
by
javiflaja
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0
1) I realised I was supposed to add RGs during alingment command only after I was long done with that step. But I imgined the tool "addorre…
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴
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
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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…
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