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Recent Replies
Comment: RNAseq of primary tumor and metastases in two different organ
by
BioinfGuru
★
1.6k
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
★
2.3k
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
•
0
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…
Comment: Bwa sampe - BGI
by
ATpoint
81k
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
by
lorena9132
•
0
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
by
BioinfGuru
★
1.6k
Take a look at [this post][1] ... it might give a clue.
Alternatively, for my installation the qcmodule is located at:
/home/bioinfguru/…
Comment: Bioinformatics_where do i start
by
BioinfGuru
★
1.6k
The [biostars handbook][1] is well worth the money
[1]: https://www.biostarhandbook.com/
Comment: Statistical Advice Needed for RNAseq Data Analysis
by
David
•
0
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
by
BioinfGuru
★
1.6k
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…
Comment: RNAseq of primary tumor and metastases in two different organ
by
BioinfGuru
★
1.6k
P-values are not corrected for the multiple comparisons inherent in differential gene expression analysis. FDR (aka qvalue) is used for sel…
Comment: CombineGVCFs vs. MergeVcfs
by
Jeremy Leipzig
22k
in the supplemental materials of that UKBB paper they actually do mention MergeVcfs but it must be a typo
Comment: add INFO tag to vcf with bcftools
by
Javier
•
0
Hi, I'm trying to do something similar, could you share the code to do what you describe.
Thanks
Comment: Visualization of PROKKA Annotation Result?
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Joe
21k
Colin's answer is essentially the right one I believe, but the more immediate consideration is: *what are you actually trying to show?*
Mo…
Comment: Bioinformatics_where do i start
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Pierre Lindenbaum
161k
https://www.biostars.org/p/9554614/ ; <br>
https://www.biostars.org/p/98983 ; <br>
https://www.biostars.org/p/9583727/ :<br>
https://www.b…
Answer: Bwa sampe - BGI
by
Pierre Lindenbaum
161k
bwa sampe produces unsorted SAM , not BAM.
converting SAM to BAM will reduce the size
sorting the BAM will reduce the size (you can …
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