0
votes
0
replies
26
views
0
votes
3
replies
149
views
updated 4 hours ago by
Alex Reynolds
35k
•
written 15 hours ago by
feather-W
•
0
0
votes
2
replies
68
views
5 hours ago by
Tully
•
0
0
votes
1
reply
86
views
0
votes
1
reply
70
views
0
votes
0
replies
57
views
9 hours ago by
camillab.
▴
140
2
votes
4
replies
276
views
updated 13 hours ago by
Pierre Lindenbaum
157k
•
written 2 days ago by
RogueBiochemist
•
0
0
votes
1
reply
103
views
0
votes
0
replies
76
views
23 hours ago by
gorizwango
▴
30
2
votes
4
replies
227
views
20 hours ago by
fifty_fifty
▴
60
0
votes
4
replies
294
views
13 hours ago by
langziv
▴
50
2
votes
7
replies
657
views
updated 10 hours ago by
Jeremy Leipzig
21k
•
written 8 days ago by
Can Abdullah
•
0
12
votes
11
replies
16k
views
10 follow
Recent Votes
Recent Locations •
All
UCLA, just now
United States, 7 minutes ago
Australia, 28 minutes ago
Canada, 33 minutes ago
United States, 1 hour ago
United States, 1 hour ago
NYC, 1 hour ago
Recent Awards •
All
Commentator to
dsull
★
4.8k
Popular Question to
natasha.sernova
★
3.9k
Popular Question to
ntsopoul
▴
50
Teacher to
benformatics
3.8k
Popular Question to
iislam
•
0
Recent Replies
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
GenoMax
134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files
by
Alex Reynolds
35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space:
```
bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
```bash
# Obtain the makefile
curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile
# Run the makefile
make vcf
```
Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
> System Information: Ubuntu 22.04 (WSL2)
>
> Shell: zsh
>
> Installation Verification: Yes, doctor.py OK
[1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File
by
Reem
•
0
Did it affect the bamtofastq output file? if so how did you solve the problem?
Thanks
Answer: How to import bigwig files into igvR
by
Trivas
★
1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
•
0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
•
0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process.
ok here is a **nextflow** based solution,(NOT tested)
workflow {
…
Comment: Assessing Rockhopper's output
by
langziv
▴
50
I see.
I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \
-a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴
980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Traffic: 1111 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6