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Comment: Limma returned only positive logFC values
by
melissachua90
▴
40
Several hundred to 10000 DEGs.
Would normalization affect logFC?
Answer: Contigs to chromosomes annotation
by
Darked89
4.3k
Not sure if it is the easiest, but you can map your new assembly to i.e. Dmel genome using LAST:
* www: https://gitlab.com/mcfrith/last …
Answer: Gene prediction software
by
Darked89
4.3k
How complete/polished is your catfish genome assembly?
Also: do you have some good quality RNA-Seq?
With a draft genome it would be…
Comment: Limma returned only positive logFC values
by
LChart
2.6k
It'd be helpful to know how many differentially expressed genes there are. If you've got a handful and they're all upregulated, I wouldn't …
Comment: variant allelic fraction
by
Ram
39k
Cross-posted on bioinfo SE: https://bioinformatics.stackexchange.com/questions/21118/how-to-calculate-the-variant-allelic-fraction-vaf
OP,…
Comment: Gene enrichment analysis with GOfuncR
by
jv
★
1.2k
how is this post different from your previous post? <https://www.biostars.org/p/9565445/#9565445>
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
by
GenoMax
129k
You can `cat` the respective R1/R2 files in same order e.g. `cat Run1_R1.fq.gz Run2_R1.fq.gz > R1.fq.gz`.
Comment: too many zeros in 16S rRNA amplicon sequencing data
by
zhangdengwei
▴
180
Exactly. I agree that this is due to the NovaSeq which is not very compatible with qimme2 DADA2 pipeline. I finally surrendered to other ap…
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
by
ev97
•
0
Thanks for your quick reply! How would you merge them?
Comment: Same GEO Accession, different SRR number, how to download this RNA-seq paired-en
by
Trivas
★
1.2k
My guess is that some samples were resequenced. I'd recommend just merging the respective R1 and R2s and treat them as one sample.
Comment: Get protein information from ensemblbacteria using interpro
by
sgiorgetti
▴
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@GenoMax Apologies for my belated reply.
Agreed, the REST endpoint above supports Ensembl IDs only. Mentioned because both the initial que…
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★
2.2k
Ah, I see. Then, no, I don't believe that this is possible with the VEP
Comment: VEP tab/vcf - Different output
by
Jeremy Leipzig
21k
I don't think that is in VCF-style coordinates which show deletions like chr1:99:AG -> A instead of chr1:100:G -> -
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴
100
Sure, here is my json file, I have 8 fastq files:
{
"atac.title" : “atac)”,
"atac.description" : “Encode”,
…
Comment: Differential protein expression analysis
by
dsull
★
4.2k
Yes, you need to log-transform.
I've had a good experience using limma for proteomics analyses (limma uses a moderated t-test).
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