User: Pascal

gravatar for Pascal
Pascal1.5k
Reputation:
1,490
Status:
Trusted
Location:
Barcelona
Last seen:
7 years, 9 months ago
Joined:
8 years, 5 months ago
Email:
p********@gmail.com

Posts by Pascal

<prev • 112 results • page 2 of 12 • next >
2
votes
4
answers
7.9k
views
4
answers
Answer: A: Choosing Window Size (Sliding Window Approach) During Cnv Analysis By Readdepth
... Very good question indeed. One usually use 100bp-window (non-overlapping windows). Please have a look to "Sensitive and accurate detection of copy number variants using read depth of coverage." (Yoon et al.), there is a good explanation of why they did use this length. ...
written 8.1 years ago by Pascal1.5k
0
votes
1
answer
1.7k
views
1
answers
Comment: C: Convert Bamtobed Score
... Whatch out Pierre: this trick doesn't output with tab-separated columns... ...
written 8.1 years ago by Pascal1.5k
3
votes
1
answer
1.7k
views
1
answers
Answer: A: Convert Bamtobed Score
... I suggest you use awk after bamToBed. If the score you want to replace is in column 4 you could use: cat your_file.bed | awk '{ print $1"\t"$2"\t"$3"\t1\t"$5"\t"$6}' ...
written 8.1 years ago by Pascal1.5k
0
votes
3
answers
6.1k
views
3
answers
Comment: C: Where Could I Download Mappability Data To Compare My Cnv Calls With?
... Thanks for the paper. Derrien is one the guy who actually produced the Mappability track from CRG institute. ...
written 8.1 years ago by Pascal1.5k
0
votes
3
answers
6.1k
views
3
answers
Comment: C: Where Could I Download Mappability Data To Compare My Cnv Calls With?
... Thanks for your answer. I didn't see "Mappability" track for hg18, but it is indeed available for hg19. ...
written 8.1 years ago by Pascal1.5k
9
votes
3
answers
6.1k
views
3
answers
Where Could I Download Mappability Data To Compare My Cnv Calls With?
... Hi. I would like to compare a set of CNV calls I have in BED file format against mappability information. Where could I find this information? (I thought it was available in UCSC track downloads). Thanks. ...
cnv written 8.1 years ago by Pascal1.5k • updated 8.1 years ago by Casey Bergman18k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: 2-3 Example Datasets (References) With Known Variants?
... You very welcome :-) You probably have seen that they release also a suite of tools. ...
written 8.1 years ago by Pascal1.5k
30
votes
4
answers
21k
views
10 follow
4
answers
Difference Between "Pipeline" And "Workflow" ?
... A quick and basic question today. I often see in literature (in particular in the context of NGS) the words "pipeline" and "workflow" used alternatively. Is there a real difference between those? ...
next-gen sequencing written 8.1 years ago by Pascal1.5k • updated 3.7 years ago by JD3e33440
1
vote
9
answers
87k
views
9
answers
Comment: C: Useful Bash Commands To Handle Fasta Files
... I like very much to have a repository of common and useful bash scripts/commands. I suggest to extend this repository to more topics like VCF, BED manipulations, etc. ...
written 8.1 years ago by Pascal1.5k
3
votes
1
answer
1.3k
views
1
answers
Answer: A: 2-3 Example Datasets (References) With Known Variants?
... Hi Angel. Please have a look to the dataset that Comple Genomics released link text "...There are also two cancer pairs including matched tumor and normal genomes derived from cell-line samples of patients with breast cancer" I hope it helps. ...
written 8.1 years ago by Pascal1.5k

Latest awards to Pascal

Supporter 7.8 years ago, voted at least 25 times.
Voter 7.8 years ago, voted more than 100 times.
Centurion 7.8 years ago, created 100 posts.
Guru 7.8 years ago, received more than 100 upvotes.
Student 8.1 years ago, asked a question with at least 3 up-votes. For Why Does Ucsc "Exons" Track Overlap With "Introns" Track?
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Convert Bamtobed Score
Student 8.1 years ago, asked a question with at least 3 up-votes. For Difference Between "Pipeline" And "Workflow" ?
Popular Question 8.1 years ago, created a question with more than 1,000 views. For Difference Between "Pipeline" And "Workflow" ?
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: 2-3 Example Datasets (References) With Known Variants?
Good Answer 8.2 years ago, created an answer that was upvoted at least 5 times. For A: Linux Distros Best Suited For Bioinformatics?
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: Linux Distros Best Suited For Bioinformatics?
Appreciated 8.2 years ago, created a post with more than 5 votes. For A: Linux Distros Best Suited For Bioinformatics?
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: Online Resources For Mouse Research
Good Answer 8.2 years ago, created an answer that was upvoted at least 5 times. For A: Online Resources For Mouse Research
Appreciated 8.2 years ago, created a post with more than 5 votes. For A: Online Resources For Mouse Research
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: Ethical Issues In Bioinformatics
Appreciated 8.2 years ago, created a post with more than 5 votes. For A: Ethical Issues In Bioinformatics
Good Answer 8.2 years ago, created an answer that was upvoted at least 5 times. For A: Ethical Issues In Bioinformatics
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: What Are The Most Common Stupid Mistakes In Bioinformatics?
Student 8.3 years ago, asked a question with at least 3 up-votes. For Where Can I Find Data Sets Of Cancer Publicly Available?
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Can'T Locate Vcf.Pm Vcftools
Teacher 8.3 years ago, created an answer with at least 3 up-votes. For A: Can'T Locate Vcf.Pm Vcftools
Student 8.4 years ago, asked a question with at least 3 up-votes. For The Meaning Of "Seq Being Reverse Complemented" In Sam Format
Popular Question 8.4 years ago, created a question with more than 1,000 views. For How To Get The "Library Insert Size" Out Of A Sam/Bam File?
Popular Question 8.4 years ago, created a question with more than 1,000 views. For Sorting Bam File For Gatk Read-Pair Walkers

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 786 users visited in the last hour