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13 results • Page
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26
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bedtools intersect by position & stand not working even with common regions
bedtools
genomic
intersect
bedops
intervals
3 hours ago by
Alewa
▴ 130
0
votes
3
replies
149
views
Getting the overlap between two GTF files
file
RNA-seq
GTF
updated 4 hours ago by
Alex Reynolds
35k • written 15 hours ago by
feather-W
• 0
0
votes
2
replies
68
views
Encountering Error while Running 'make vcf' in Biostar Handbook
bugfix
biostarhandbook
vcf
5 hours ago by
Tully
• 0
0
votes
1
reply
86
views
How to import bigwig files into igvR
bigwig
igvr
updated 6 hours ago by
Trivas
★ 1.5k • written 9 hours ago by
ntsopoul
▴ 50
0
votes
1
reply
70
views
MAKER: WARNING: Could not get initialization lock. Trying Again...
gene
annotation
MAKER
prediction
updated 2 hours ago by
GenoMax
134k • written 9 hours ago by
memy
▴ 20
0
votes
0
replies
57
views
TPM from STAR output without re-allign the file using RSEM or Salmon
bulkRNASEQ
STAR
RSEM
9 hours ago by
camillab.
▴ 140
2
votes
4
replies
276
views
Automate the Splitting of a VCF File by Sample (bcftools)
bcftools
vcf
updated 13 hours ago by
Pierre Lindenbaum
157k • written 2 days ago by
RogueBiochemist
• 0
0
votes
1
reply
103
views
Unable to install HorvathMammalMethylChip40manifest packages
r
programming
updated 14 hours ago by
ATpoint
77k • written 16 hours ago by
Nibedita
• 0
0
votes
0
replies
76
views
TEtranscripts Tool in Galaxy
RNAseq
Transposable_Elements
TE_Transcripts
23 hours ago by
gorizwango
▴ 30
2
votes
4
replies
227
views
Subclustering of intergated cells from scRNA-seq data
scRNA-seq
Seurat
20 hours ago by
fifty_fifty
▴ 60
0
votes
4
replies
294
views
Assessing Rockhopper's output
transcriptome
Rockhopper
RNA-seq
de-novo-assembly
13 hours ago by
langziv
▴ 50
2
votes
7
replies
657
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 10 hours ago by
Jeremy Leipzig
21k • written 8 days ago by
Can Abdullah
• 0
12
votes
11
replies
16k
views
10 follow
Retrieve The Reads And Fastq From Bam File
samtools
updated 6 hours ago by
Reem
• 0 • written 11.0 years ago by
rehma.ar
▴ 290
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A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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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?
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