Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In

User: trausch

gravatar for trausch
trausch • 1.1k
Reputation:
1,130
Status:
Trusted
Location:
Germany
Website:
http://tobiasrausch.gi...
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
3 years, 5 months ago
Email:
r*********@gmail.com

Posts by trausch

<prev • 120 results • page 1 of 12 • next >
0
votes
2
answers
112
views
2
answers
Comment: C: find coverage of specific exomes from a bam file
... Osx builds are skipped for performance reasons in the Bioconda versions, linux-64 is the default platform. You can either build from source on osx (requires boost library) or use [this minimal docker container of Alfred][1] (if you are familiar with docker). [1]: https://hub.docker.com/r/trausch/ ...
written 2 days ago by trausch • 1.1k
2
votes
2
answers
112
views
2
answers
Answer: A: find coverage of specific exomes from a bam file
... [Alfred][1] can be used for that: alfred count_dna -i exome.bed.gz -o coverage.gz input.bam [1]: https://github.com/tobiasrausch/alfred ...
written 6 days ago by trausch • 1.1k
1
vote
1
answer
173
views
1
answers
Answer: A: Majority consensus from bam file
... This should work using [Alfred][1] ./alfred consensus -f bam -t ont -p chr1:218992200 The alignment scoring depends on the sequencing technology. If you have phased SNPs and long reads you should split the BAMs into haplotypes prior to the consensus computation. [1]: https://github.com/tob ...
written 4 weeks ago by trausch • 1.1k
0
votes
2
answers
201
views
2
answers
Comment: C: Other then picard better way to calculate insertmetrics from a bam file ?
... Thanks, did alfred work? ...
written 6 weeks ago by trausch • 1.1k
0
votes
2
answers
201
views
2
answers
Answer: A: Other then picard better way to calculate insertmetrics from a bam file ?
... Another option is [Alfred][1]. We provide example quality control files for different sequencing assays (DNA-Seq whole-exome, ATAC-Seq, ...) and different sequencing technologies (Illumina, ONT, PacBio) at the [companion web application][2] so you can have a look if that's what you are looking for ( ...
written 6 weeks ago by trausch • 1.1k
0
votes
2
answers
130
views
2
answers
Answer: A: DNA sequences from the origins of replication.
... [Repli-Seq][1] can be used to map origins of replication. For humans there are likely cell-type-specific replication programs. [1]: http://www.pnas.org/content/107/1/139 ...
written 6 weeks ago by trausch • 1.1k
1
vote
1
answer
142
views
1
answers
Answer: A: Human CNV VCF for Trios from whole-genomes
... [Delly][1] SV calls for the [HGSVC trios][2] are available [here][3]. [1]: https://github.com/dellytools/delly [2]: https://www.biorxiv.org/content/early/2018/06/13/193144 [3]: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/hgsv_sv_discovery/working/20160930_pre_ashg_calls/2016100 ...
written 9 weeks ago by trausch • 1.1k
0
votes
2
answers
155
views
2
answers
Comment: C: Identification of break points for a balanced translocation
... You can just extract the 2 translocated chromosomes of interest: samtools view -b chrA chrB > subset.bam samtools index subset.bam Or if you know the approximate regions: samtools view -b chrA:10000000-20000000 chrB:50000000-60000000 > subset.bam samtools index subset.bam ...
written 9 weeks ago by trausch • 1.1k
1
vote
2
answers
155
views
2
answers
Answer: A: Identification of break points for a balanced translocation
... If you have paired-end whole genome data you can use [Delly][1]. [1]: https://github.com/dellytools/delly ...
written 9 weeks ago by trausch • 1.1k
0
votes
3
answers
1.8k
views
3
answers
Answer: A: Software to analyse mutations in sanger sequencing files
... [Indigo][1] is open-source. Indigo analyses sanger sequencing files (ab1), separates het. InDel mutations and aligns the sequences to a reference genome, wildtype chromatogram or custom fasta file. It also works for homozygous mutations or SNP identification in general. [1]: https://gear.embl.de/ ...
written 10 weeks ago by trausch • 1.1k

Latest awards to trausch

Scholar 9 weeks ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Centurion 4 months ago, created 100 posts.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Get trace data for all four bases from ab1 file
Guru 5 months ago, received more than 100 upvotes.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 9 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Good Answer 10 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 10 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 10 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 14 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 15 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 16 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Appreciated 16 months ago, created a post with more than 5 votes. For A: list of gene or transcript IDs and their length
Scholar 16 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 21 months ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Scholar 2.8 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Methods of classifying, not detecting, structural variation?
Scholar 2.8 years ago, created an answer that has been accepted. For A: updating vcf file from rsIDs of dbsnp138 to dbsnp144
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2161 users visited in the last hour