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Answer: List of species in RepeatMasker Tool (species parameter)
by
Bioinfotec
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From 4.1.1 version, The utilities 'queryTaxonomyDatabase.pl' and 'queryRepeatDatabase.pl' are no
longer included, since that data…
Comment: RNAseq of primary tumor and metastases in two different organ
by
matteo.levorato
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0
Yeah, I heard that for cycle are not super suggested in R. I can't use tibble since my bone df has a different size than lung df..
However …
Comment: SnpEff annotates coding duplication as intronic?
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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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dsull
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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…
Comment: Rename multiple fastq.gz files
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Jérémie
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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…
Comment: RNAseq of primary tumor and metastases in two different organ
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BioinfGuru
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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
by
bk11
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This will be a very rough way of doing it-
#listing the fastq files
ls *fastq.gz
JM1-44589688_S693_L001_R1_001.fastq.gz JM110-…
Comment: RNAseq of primary tumor and metastases in two different organ
by
matteo.levorato
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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…
Comment: Bwa sampe - BGI
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Hello, thank you very much for your response. I was referring more to using these options:
-a INT Maximum insert size for a read pair …
Comment: gene body coverage with RSeqQC
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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:
/home/bioinfguru/…
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BioinfGuru
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The [biostars handbook][1] is well worth the money
[1]: https://www.biostarhandbook.com/
Comment: Statistical Advice Needed for RNAseq Data Analysis
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David
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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 …
Comment: RNAseq of primary tumor and metastases in two different organ
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BioinfGuru
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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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BioinfGuru
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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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