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Recent Replies
Answer: What type of database does gnomAD use?
by
Jeremy Leipzig
21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
by
Basti
★
1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Filter InterProScan output for a specific function
by
jv
▴
780
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data?
by
STARDUST
•
0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans
by
GenoMax
125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
by
jv
▴
780
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf>
- Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content
by
jv
▴
780
I think this is to be expected based a report I was able to find online
<https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
Comment: RNA Editing data from RNA-seq
by
Genetics
•
0
Thank you so much for your kind reply and for helping a bioinformatics beginner like me.
Can I use **bowtie2** tools for allignment and th…
Comment: fastqc: Per base sequence content
by
khoojj
•
0
Yes, I have proceed with analysis but I wonder if it is necessary to remove the first 10 or so bp from the reads.
I have checked that NEBN…
Comment: Novogene somatic results with GATK mutect2
by
GenoMax
125k
Did you look in the header of the provided VCF to see if any information has been encoded there (e.g. command line/options used).
Comment: RNASeq differential expression masked by pathways disregulation
by
Gama313
▴
110
That's exactly what I've done. However the dispersion is really high (primary samples) and the total number of samples seems really low to…
Comment: fastqc: Per base sequence content
by
GenoMax
125k
If the library was made using tagmentation then you will see that pattern.
Flag warnings on FastQC do not immediately indicate that the da…
Answer: What type of database does gnomAD use?
by
Matthias Zepper
2.9k
I suppose there are multiple? Queries via Hail are very likely run against a [Matrix Table][1], but the web application likely uses a diffe…
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