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Answer: How can I convert this pairwise format to fasta?
Answer: How can I convert this pairwise format to fasta?
Piping bowtie2 output directly into BAM
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: RNA Editing data from RNA-seq
Comment: RNA Editing data from RNA-seq
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Answer: What type of database does gnomAD use?
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If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
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You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
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This post does not fit the theme of this forum.
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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?
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STARDUST
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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 …
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See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
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- 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
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jv
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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
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GenoMax
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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
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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
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khoojj
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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…
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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).
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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
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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?
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Matthias Zepper
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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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