User: abedkurdi10

gravatar for abedkurdi10
abedkurdi1030
Reputation:
30
Status:
New User
Location:
Last seen:
1 week, 1 day ago
Joined:
4 years, 2 months ago
Email:
a**********@gmail.com

Posts by abedkurdi10

<prev • 39 results • page 1 of 4 • next >
0
votes
1
answer
72
views
1
answers
Answer: A: How to call CNV without normal samples
... You can use `cnvkit` tool to call somatic CNVs. Don't forget to use `--drop-low-coverage` argument too. ...
written 9 days ago by abedkurdi1030
0
votes
3
answers
103
views
3
answers
Answer: A: intersect two file
... Or You can use `dplyr` R package to do the intersection. ...
written 9 days ago by abedkurdi1030
0
votes
1
answer
127
views
1
answers
Answer: A: RNA-seq Infer experiment wrong strandeness information
... It seems that there is more rRNA sequences. I downloaded `rmsk` bed file from UCSC and removed all reads covering those Repeating Elements (including and not limited to rRNA, tRNA...), then I run again `infer_experiment` and everything went well. ...
written 5 months ago by abedkurdi1030
0
votes
1
answer
127
views
1
answers
Comment: C: RNA-seq Infer experiment wrong strandeness information
... I will have a look on them. Actually, It's mouse data. ...
written 5 months ago by abedkurdi1030
0
votes
1
answer
127
views
1
answer
RNA-seq Infer experiment wrong strandeness information
... Hello everyone, I have received recently eight RNA-seq samples. We know that the reads are `reversely stranded`. After aligning those samples to their reference genome, I run `infer_experiment` on the alignment data just to make sure everything is fine. Five samples out of eight showed that they ...
infer_experiment rna-seq rseqc written 5 months ago by abedkurdi1030
0
votes
1
answer
328
views
1
answers
Comment: C: Interval list for GATK tool Haplotype Caller
... Yes, for every gene or for genes of interest ...
written 5 months ago by abedkurdi1030
0
votes
1
answer
328
views
1
answers
Answer: A: Interval list for GATK tool Haplotype Caller
... As I know, intervals in HaplotypeCaller are BED files (Genomic positions). You specify the regions where to call variants. ...
written 5 months ago by abedkurdi1030
0
votes
2
answers
241
views
2
answers
Comment: C: Conversion of Vep.vcf to MAF format?
... but this is the same vcf2maf.pl which requires vep to run ...
written 6 months ago by abedkurdi1030
0
votes
2
answers
241
views
2
answers
Comment: C: Conversion of Vep.vcf to MAF format?
... Maybe you can use `bcftools +split-vep` and extract the variants in tabulated format with specific order of the fields. ...
written 6 months ago by abedkurdi1030
1
vote
2
answers
241
views
2
answers
Answer: A: Conversion of Vep.vcf to MAF format?
... While it is no more maintained, but try this: `https://github.com/cbare/vcf2maf` ...
written 6 months ago by abedkurdi1030

Latest awards to abedkurdi10

Popular Question 3 months ago, created a question with more than 1,000 views. For Optimal number of samples needed to detect a variant from panel sequencing
Popular Question 9 months ago, created a question with more than 1,000 views. For raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
Popular Question 3.7 years ago, created a question with more than 1,000 views. For raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Thresholds to filter out variants from vcf file
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Clinical significance explanation
Popular Question 3.7 years ago, created a question with more than 1,000 views. For VCF file re-header

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1658 users visited in the last hour