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Recent Votes
A: What Is The Sequencing 'Depth' ?
A: Read Duplicates
A: Read Duplicates
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
Comment: Only one read per run - Trying to use CellRangerv7
Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
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Recent Replies
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you !!
Answer: Can I have multiple active GDC download tokens?
by
Zhenyu Zhang
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You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
Comment: Parsing fasta file by coordinates
by
sorrymouse
▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did run the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
Comment: Nanopore data filtering using fastp
by
GenoMax
140k
You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I was using it but the output file was too big pipe the output
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Share code and an example please.
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
▴ 10
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
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