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Recent Replies
Comment: SNV, CNA, SV
by
Vincent Laufer
★
2.2k
what exactly do you want to show about them. do you want to show the order in which they arose? or epistasis between them> ? or any other p…
Comment: Why weblogo of biopython doesn't work?
by
Plus
•
0
Yes. I can try the web version of WebLogo, but I just want to know what kind of problem can induce to make a corrupted file by using Motif.…
Comment: Difference between clusterProfiler and gProfileR
by
Arup Ghosh
3.0k
> The GO terms output by gprofileR are generally quite similar to those
> output by clusterProfiler, but there are small differences due to…
Comment: Why weblogo of biopython doesn't work?
by
Arup Ghosh
3.0k
The `weblogo` module uses the web version of weblogo service and it seems the module is not working as intended. Instead of returning an im…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
appropiate
▴
40
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and…
Comment: Extract sequences from a list of ID
by
GenoMax
119k
You need to remove `>` from ID's as the warning tells you to do.
Comment: The best way to get gene lengths for 15K+ genes?
by
manaswwm
▴
260
From my previous experiences in retrieving data in bulk from biomaRt/Ensembl - it is always better to partition your data into batches befo…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
cmdcolin
★
2.3k
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped …
Answer: download just a chromosome from SRA toolkit
by
ATpoint
64k
No, it is not possible since fastq are raw data without alignment information, hence without chromosomal information.
Answer: download just a chromosome from SRA toolkit
by
shelkmike
▴
660
No, its impossible. Sequencing reads in SRA are not partitioned by chromosomes.
Comment: Extract sequences from a list of ID
by
Neel
▴
20
Hi, i want to extract seq from list of id but Seqkit gives this below error and empty output file generated
[WARN] symbol ">" detected…
Answer: Convert mpileup file into dataframe
by
ATpoint
64k
No, don't do any custom data fiddling. Follow the manual of bcftools for variant calling, it covers all you need: https://samtools.github.i…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ
by
GenoMax
119k
You can open multiple instances of IGV and display multiple genome alignments.
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
by
chronotope
▴
10
Thanks for the headsup about the positive control! Any way I can add another pair of reads to the bam file, containing my positive control …
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