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Comment: RNAseq of primary tumor and metastases in two different organ
Comment: Bioinformatics_where do i start
Comment: Can I compare kallisto counts from samples with different amount of reads?
Comment: RNAseq of primary tumor and metastases in two different organ
Comment: CombineGVCFs vs. MergeVcfs
Comment: Bioinformatics_where do i start
Answer: Bwa sampe - BGI
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Recent Replies
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?
by
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
by
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 …
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
by
Bikram Kumar
• 0
Hi! Should I delete the stack exchange post? I didn't know that cross posting is bad. [https://meta.stackoverflow.com/a/425789/5140632][1] …
Answer: Visualization of PROKKA Annotation Result?
by
colindaven
6.3k
You need a genome browser and you can probably use GBK or gff3 format. Here are some suggestions - I like JBrowse best, Artemis in its …
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