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Popular Question to
I0110
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always_learning
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graeme.thorn
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Recent Replies
Answer: enrichr
by
Laura
▴
20
Use it through [gget enrichr][1] for super easy use!
[1]: https://github.com/pachterlab/gget
Comment: DESeq2 use of factors for colData
by
swbarnes2
12k
I believe it will try to make a linear correlation between the logs of the counts and your numerical colData. But it's hard to know withou…
Comment: Difference in total gene counts between samples
by
swbarnes2
12k
I think it's glaringly obvious that library size is driving your first PC. I would not be at all confident that the typical techniques wil…
Answer: Retrieving ensembl protein length with biomart
by
Laura
▴
20
*[gget][1] seq* will return the nucleotide (option "gene") or amino acid (option "transcript") sequence and sequence length for any Ensembl…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Pierre Lindenbaum
145k
`$1`: https://www.gnu.org/software/gawk/manual/gawk.html#Fields
`/^@/`: https://www.gnu.org/software/gawk/manual/gawk.html#Regexp-Usage
`…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
I0110
▴
120
What is the "$1 ~ /^@/'" part for? Thanks!
Answer: fastq.gz download error
by
GenoMax
115k
This dataset appears to have been released just a few days back (20th May) so it may not be fully ready to download from ENA.
$ curl …
Comment: fastq.gz download error
by
nishimalhotra2612
▴
10
I m downloading it directly from ENA database
Generated fastq files:FTP
And the operating system is windows 11
It's not the error but …
Comment: fastq.gz download error
by
lieven.sterck
13k
you'll need to provide some more (crucial) information here: how are you downloading it? (program? OS?) , what is the error you get? ... th…
Comment: snakemake r script
by
nishimalhotra2612
▴
10
thanks i will modify script and will install the needed package
Comment: Third Quartile (Q3) for RNAseq data
by
Leo
•
0
I read that it is a common approach to use ConsensusClusterPlus. I am trying to figure out, are TCGA data_mrna_seq_v2_rsem.txt data already…
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir
by
ATpoint
61k
Indeed, good catch!
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir
by
rpolicastro
8.2k
If you want the exact intron ranges you would need to modify the above but by looking per transcript. Doing it per gene would give you regi…
Comment: PCA plot interpretation after accounting for batch effects with SVA
by
rpolicastro
8.2k
There doesn't appear to be an appreciable separation between the two conditions for most of your samples. Instead of immediately going to S…
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