User: trausch
trausch • 1.0k
- Reputation:
- 1,020
- Status:
- Trusted
- Location:
- Germany
- Website:
- http://tobiasrausch.gi...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 21 hours ago
- Joined:
- 3 years, 1 month ago
- Email:
- r*********@gmail.com
Posts by trausch
<prev
• 104 results •
page 1 of 11 •
next >
0
votes
0
answers
319
views
0
answers
Comment:
C: repli-seq analysis pipeline
... It depends on the input BAMs. ...
written 19 days ago by
trausch • 1.0k
0
votes
0
answers
319
views
0
answers
Comment:
C: repli-seq analysis pipeline
... As far as I remember I used the normalization from [this paper][1].
[1]: http://www.pnas.org/content/107/1/139 ...
written 19 days ago by
trausch • 1.0k
0
votes
0
answers
319
views
0
answers
Comment:
C: repli-seq analysis pipeline
... I did create a very basic [Repli-Seq analysis workflow][1] a while ago.
[1]: https://github.com/tobiasrausch/repliseq ...
written 23 days ago by
trausch • 1.0k
0
votes
2
answers
108
views
2
answers
... [Alfred][1] should work
alfred count_jct -g Homo_spaiens.GRCh37.75.gtf.gz input.star.bam
[1]: https://github.com/tobiasrausch/alfred ...
written 4 weeks ago by
trausch • 1.0k
0
votes
3
answers
327
views
3
answers
Answer:
A: ATAC-seq DE analysis
... Another ATAC-Seq pipeline is available [here][1]. As part of the pipeline a count matrix is generated and an Rscript template for differential peak calling is part of the pipeline ([script is here][2]).
[1]: https://github.com/tobiasrausch/ATACseq
[2]: https://github.com/tobiasrausch/ATACseq/b ...
written 5 weeks ago by
trausch • 1.0k
0
votes
0
answers
192
views
0
answers
... Number of hets, hom. ref. and hom. alt. in a given region
bcftools stats -r chr1:23000-26000 -s -
You are probably interested in runs of homozygosity
bcftools roh
...
written 8 weeks ago by
trausch • 1.0k
2
votes
2
answers
187
views
2
answers
... bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/AF:=INFO/EUR_AF my_vcf > EUR_AF.vcf
...
written 9 weeks ago by
trausch • 1.0k
3
votes
2
answers
187
views
2
answers
...
bcftools annotate -a EUR.chr13.phase1.vcf.gz -c INFO/AF ...
written 9 weeks ago by
trausch • 1.0k
1
vote
0
answers
221
views
0
answers
Comment:
C: Weird insert size distribution
... I suspect your read-length is ~135bp? The insert size is usually the outward distance so the lower bound is the read-length. [Alfred][1] (disclaimer: my own tool) splits the insert size by all possible 4 types of read pair orientations so this will at least tell you if you have the standard illumina ...
written 10 weeks ago by
trausch • 1.0k
1
vote
1
answer
178
views
1
answers
Comment:
C: calculate ti/tv ratio in WGS data
... The expected ratio of transitions to transversions in the whole genome is near 2.0 for humans. ...
written 10 weeks ago by
trausch • 1.0k
Latest awards to trausch
Centurion
4 weeks ago,
created 100 posts.
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Good Answer
8 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Get trace data for all four bases from ab1 file
Guru
8 weeks ago,
received more than 100 upvotes.
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Scholar
6 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: Get trace data for all four bases from ab1 file
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: list of gene or transcript IDs and their length
Scholar
6 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: list of gene or transcript IDs and their length
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Scholar
11 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar
12 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Appreciated
12 months ago,
created a post with more than 5 votes.
For A: list of gene or transcript IDs and their length
Scholar
12 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar
17 months ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher
2.5 years ago,
created an answer with at least 3 up-votes.
For A: Methods of classifying, not detecting, structural variation?
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 644 users visited in the last hour