User: roalva1

gravatar for roalva1
roalva180
Reputation:
80
Status:
Trusted
Location:
Spain
Last seen:
4 days, 8 hours ago
Joined:
5 years, 10 months ago
Email:
r******@gmail.com

about me

Posts by roalva1

<prev • 31 results • page 1 of 4 • next >
1
vote
0
answers
63
views
0
answers
Classify benign tumor vs malign tumor
... Hello, I am using the Trusight Tumor 170 kit from Illumina. I have sequenced 10 benign tumor samples and 10 malign tumos samples. I would like to create a classifier based on snps and indels (what Illumina calls small variants). I have already some snps and indels that belongs only to the malign s ...
indels snps tumor written 16 days ago by roalva180
0
votes
1
answer
101
views
1
answers
Comment: C: nonamecheck not working in bedtools coverage
... Yes, I don't have any chrM regions in my bed file, but I do have in my bam. The message of bedtools should be a warning but it is not. Bedtools stops and the coverage in chrX regions are not calculated. ...
written 24 days ago by roalva180
0
votes
1
answer
101
views
1
answers
Comment: C: nonamecheck not working in bedtools coverage
... My bed file doesn't have any region in chrMT nor chrM ...
written 24 days ago by roalva180
0
votes
1
answer
101
views
1
answers
Comment: C: nonamecheck not working in bedtools coverage
... No no, I have got just a bam ...
written 24 days ago by roalva180
0
votes
1
answer
101
views
1
answers
Comment: C: nonamecheck not working in bedtools coverage
... This has solved my problem, but still, with bedtools 2.17 we didn't need this, and I think it is not intuitive. ...
written 24 days ago by roalva180
0
votes
1
answer
101
views
1
answers
Comment: C: nonamecheck not working in bedtools coverage
... Wouldn't be -nonamecheck enaugh for this? -nonamecheck For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. "chr1" vs "chr01". ...
written 24 days ago by roalva180
3
votes
1
answer
101
views
1
answer
nonamecheck not working in bedtools coverage
... Hello, I am running this command line in bedtools 2.27.1 bedtools coverage -nonamecheck -d -sorted -a file.bed -b file.bam > file.cov and I get this error ERROR: Database file file.bam contains chromosome chrM, but the query file does not. Please rerun with the -g option f ...
bedtools written 24 days ago by roalva180 • updated 24 days ago by Ram16k
1
vote
0
answers
113
views
0
answers
change temp folder in cwl
... Hello, is there any way I can change temp folder to a class Workflow cwl file? or inside a CommandLineTool class? Thanks ...
commonworkflowlanguage cwl written 26 days ago by roalva180
0
votes
1
answer
170
views
1
answers
Comment: A: does bcftools has anything like vcf-check?
... I've just discovered a truncated file. Sorry!!!! ...
written 6 weeks ago by roalva180
0
votes
1
answer
128
views
1
answer
Allele Frequency(AF) for male and female samples
... Hello, I am trying to compute AF for male and female samples. I know bcftools is able to do it, but I am not sure how it behaves for next case. If I have two samples: - chromX pos 10 Female 0/1 - chromX pos 10 Male 1/1 As you all know, Male has only one chrom X, but normally the vcf software call ...
vcf bcftools written 6 weeks ago by roalva180 • updated 5 weeks ago by finswimmer3.6k

Latest awards to roalva1

Popular Question 4 months ago, created a question with more than 1,000 views. For Associate Supporting Reads Of Fasta File With The Structural Variation
Popular Question 5 months ago, created a question with more than 1,000 views. For Associate Supporting Reads Of Fasta File With The Structural Variation
Popular Question 15 months ago, created a question with more than 1,000 views. For Pindel Is Not Detecting Long Insertions
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Pindel Is Not Detecting Long Insertions
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Compilation Errors Tigra-Sv

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 707 users visited in the last hour