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Recent Replies
Comment: SnpEff annotates coding duplication as intronic?
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Ram
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Can you show us the output from VEP and snpEff? They could be annotating two different transcripts.
EDIT: I ran VEP quickly on this varian…
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Honestly, any popular aligner will do: STAR, bowtie2, bwa, etc. Just make a FASTA file containing your sequences of interest, build an inde…
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Thank you! Just a stupid question, when I run this command it gives me the list of the names expected but does not actually change the name…
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That's normal. Anything lower than the lower limit of R's numerical value range is rounded to 0. No resolution is required. Just be careful…
Comment: Rename multiple fastq.gz files
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This will be a very rough way of doing it-
#listing the fastq files
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Comment: RNAseq of primary tumor and metastases in two different organ
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on top of this I have many genes with a padj equal to zero, is this coming from an error or it's just that the value is too small for RStud…
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Honestly, use bwa mem like everyone else and call it a day.
bwa mem ref.fa X1.fq.gz X_2.fq.gz | samtools sort -o sorted.bam
See the b…
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Hello, thank you very much for your response. I was referring more to using these options:
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Take a look at [this post][1] ... it might give a clue.
Alternatively, for my installation the qcmodule is located at:
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The [biostars handbook][1] is well worth the money
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Thank you @atpoint for your reply, but I think I didn't explain myself clearly. Initially, I compared my two datasets to their control and …
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Most advise to avoid For Loops in R (don't ask me why, unexpected results and behaviours, poor efficiency I think). I would use tidyverse f…
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P-values are not corrected for the multiple comparisons inherent in differential gene expression analysis. FDR (aka qvalue) is used for sel…
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Hi, I'm trying to do something similar, could you share the code to do what you describe.
Thanks
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