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Recent Replies
Comment: DEGseq - 3 conditions
by
pingu77
▴
10
thank you! But after I should take the intersection of the genes that are DE in resB_A and resC_A, right? thank you!
Comment: How to convert Ensemble Gene IDs to gene symbols or Entrez Gene IDs?
by
Ram
37k
I'm moving Laura's "answer" to a comment until it is edited with sufficient detail to be a fully formed answer.
Comment: no output from GATK CombineGVCFs
by
liyong
•
0
Thanks for your comments.
The CombineGVCFs commands are inside a shell script, when I run the script, I use "nohup ./combine.sh >& combin…
Comment: no output from GATK CombineGVCFs
by
Pierre Lindenbaum
149k
> and the log file didn't show any error.
which log file ?
Retry with
gatk --java-options "-Xmx5g -Djava.io.tmpdir=." CombineGV…
Comment: DEGseq - 3 conditions
by
Shred
▴
870
If samples are indipendent each other, it's fine to have a design column (named here `condition`) with the three factors (A,B,C) that could…
Comment: For loop rna sequencing alignment
by
kcarery
•
0
It contacts samples that are set up like this "Sample345.fastq" and its all listed
Comment: DEGseq - 3 conditions
by
pingu77
▴
10
thank you for your help! A,B,C are three states of a disease. I would be interested to find the genes that are consistently differentially …
Answer: random list of coordinates of different lengths
by
mmmmcandrew
▴
150
There are a couple of different ways to approach this, I think, depending on what you have on hand. If you already have a set of coordinate…
Comment: DEGseq - 3 conditions
by
Shred
▴
870
Add more details about the design. Is something like `disease`-`control`-`disease+drug`? Do you expect that condition `B` would differ from…
Comment: Error in using the MetaSubtract package
by
Khaleesi95
▴
20
It still does not work and I got the same error message
Comment: For loop rna sequencing alignment
by
Pierre Lindenbaum
149k
> Is it super beneficial for longer pipelines?
definitively
https://pubmed.ncbi.nlm.nih.gov/28398311/
> Nextflow enables reproducible …
Comment: Error in using the MetaSubtract package
by
zx8754
11k
I think `alternative_headers.txt` needs a header row, try adding "col1 col2" in the first row.
Comment: Use biomart getSequence to obtain cDNA sequence based on exon coordinates obtain
by
jv
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550
> For some reason I cannot receive the cdna using the code abov, however if use the ensemble ID, I can obtain cDNA, but thats not what i wa…
Comment: For loop rna sequencing alignment
by
iraun
4.8k
Can you copy-paste the content of `MatchedFastqList.txt`?
Comment: For loop rna sequencing alignment
by
kcarery
•
0
Sorry, I was rushing I got this error
EXITING because of fatal input ERROR: could not open readFilesIn=Read1
It also is not going do…
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