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Recent Replies
Answer: ERROR running Cuffmerge in referecne based RNA-SEQ analysis?
by
Motiar
•
0
I am also facing this problem. Did you get any solution?
cuffmerge -g /mnt/c/Desktop/Bioinformatic/Genome_seq/hg38.refGene.gtf -p 8 /mn…
Comment: Salmon Index
by
GenoMax
129k
GENCODE is in reference to human data. GENCODE only deals with human, mouse data.
You can use the Arabidopsis genome from Ensembl.
Not s…
Comment: gatk Hardfilter Error
by
Pierre Lindenbaum
154k
the formatting is missing in your question. how do you break lines ? did you add a antislash at the end of the lines ? didn't you forgot th…
Comment: Salmon Index
by
ashleymb1116
•
0
Thank you! I've made the decoy before, but I'm trying to redo it since I believe the first time I completed this incorrectly. The page Salm…
Comment: How to make a dotplot for bulk RNA average expression ?
by
LionisOne
•
0
@Trivas Thank you very much for your reply. if you don't mind could you share the script. Because its showing the dot in my plot, but I wou…
Answer: How to deal with duplicated gene IDs in TCGA RNA expression data?
by
Zhenyu Zhang
▴
800
Where did you get the data from? which reference build and gene model is it using?
There are many versions of TCGA expression data around…
Comment: gatk Hardfilter Error
by
bestone
▴
10
A USER ERROR has occurred: Argument output was missing: Argument 'output' is required.
**************************************************…
Answer: How to make a dotplot for bulk RNA average expression ?
by
Trivas
★
1.1k
You'll want to use the `pivot_longer` function in R so that you have three columns: 1) gene, 2) condition, 3) value. You can then use ggplo…
Answer: Salmon Index
by
GenoMax
129k
> can I just use the cDNA file from Ensembl as mentioned above
Yes you can. That said the recommendation from `salmon` devs is to use the …
Comment: Dada2 in Qiime2: losing reads during merging
by
andres.firrincieli
3.3k
How long was the amplicon?
If the amplicon is longer than the sum of the two read lengths, the R1 and R2 reads will not merge. By default,…
Comment: Converting RefSeq protein accession IDs into entreZ IDs
by
Pegasus
▴
90
Thank you @genomax, since efetch function is not supported by the HPC I am working on, I replaced it with the command below;
curl …
Comment: How extract specific SNP position from the bed file-Bedtools
by
LionisOne
•
0
@Pierre Lindenbaum Thanks a lot! Its a great help! I will check and let you know.
Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If
by
Joe
21k
Sounds like you might be better off using something like Mol*:
https://academic.oup.com/nar/article/49/W1/W431/6270780?login=false
https://…
Comment: how to intersect multiple bed files and get results in uncollapsed genomic inter
by
Alewa
▴
110
thank you so much Alex!
Comment: Regular Expression for conversion
by
Joe
21k
Are *all* of your long-form references of *exactly* that format? If not this will be nigh-on impossible.
This is a (non-optimal) regex whi…
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