User: rbagnall
rbagnall • 1.5k
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Posts by rbagnall
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2
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... Lets look at a gene on the X chromosome, say [F8][1]
There is a variant at `X-154065843-G-A`, which is found in 103 males in the exome data and 92 males in the genome data, giving a total of 195 males who have this variant and are hemizygous.
Now lets get the male allele count (thus number of hemi ...
written 21 hours ago by
rbagnall • 1.5k
1
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1
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88
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1
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Comment:
C: Flanking sequence retreival
... Samtools
time samtools faidx Homo_sapiens_assembly38.fasta chr8:300000-300050
>chr8:300000-300050
GACCACTTGTTCTGCATTTTCTCCATCTTCCTTGTGATTAGAAACCTCAAA
real 0m0.174s
user 0m0.003s
sys 0m0.024s
Bedtools
time bedtools getfasta -fi Homo_sapiens_assembly38.fa ...
written 5 days ago by
rbagnall • 1.5k
1
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1
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88
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1
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Answer:
A: Flanking sequence retreival
... Extract subsequence from indexed reference sequence using [samtools faidx][1].
samtools faidx your.fasta chrX:start-end
[1]: http://www.htslib.org/doc/samtools-faidx.1.html ...
written 6 days ago by
rbagnall • 1.5k
2
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1
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... From the UK biobank "The UK Biobank 50k WES FE dataset is incorrectly mapped in a non-alt-aware manner."
See the paper describing the issue [here][1] (BioRxiv)
Download the pdf comment/response from the UK Biobank [here][2]
[1]: https://www.biorxiv.org/content/10.1101/868570v1
[2]: https: ...
written 6 weeks ago by
rbagnall • 1.5k
2
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1
answer
147
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1
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... Sorry.., you are right, that was for vcf files, but the principal is the same for BAM files.
You will never which T was deleted. The convention is to left align indels at these positions in each read, and this can be done on BAM files using, for example, the GATK [LeftAlignIndels][1] tool.
For som ...
written 7 weeks ago by
rbagnall • 1.5k
0
votes
1
answer
147
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1
answers
... [left align indels][1]
[1]: https://www.biostars.org/p/66843/ ...
written 7 weeks ago by
rbagnall • 1.5k
1
vote
1
answer
99
views
1
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... You want to pass the first 10,000 scaffolds in a text file called an [interval list][1]
`-L path/to/my_interval.list`
Where an interval list file to include the first four scaffolds would look like:
`scaffold1`
`scaffold2`
`scaffold3`
`scaffold4`
This will give a single g.vcf for the firs ...
written 9 weeks ago by
rbagnall • 1.5k
1
vote
0
answers
149
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0
answers
... Are you using intervals in the format chrY:XXXX-XXXX ?
The older versions of gnomAD were mapped to hg19, with chromosome names like 1,2,3,X,Y
The new version 3 of gnomAD is mapped to GRCh38, with chromosome names like chr1, chr2, chrX, chrY ...
written 12 weeks ago by
rbagnall • 1.5k
1
vote
2
answers
359
views
2
answers
Answer:
C: awk extract certain line
... In addition to the excel line ending issue, your grep command won't work because of the `-w` (grep the exact match). If you remove the `-w` then
TRINITY_DN100000_c1_g1
of file1.txt will pick out
TRINITY_DN100000_c1_g1_1
TRINITY_DN100000_c1_g1_2
TRINITY_DN100000_c1_g1_3
of file2. ...
written 5 months ago by
rbagnall • 1.5k
2
votes
1
answer
253
views
1
answers
... Precisely! In this case it is a deletion of 3 base pairs in the coding region of ROBO2 (ACAG goes to A by loss of CAG). Therefore it is an 'in-frame' deletion, which causes the protein to be shortened by one amino acid residue. ...
written 6 months ago by
rbagnall • 1.5k
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Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Scholar
3 months ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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3 months ago,
created a comment with at least 3 up-votes.
For C: How to extract specific chromosome from vcf file
Centurion
17 months ago,
created 100 posts.
Good Answer
21 months ago,
created an answer that was upvoted at least 5 times.
For A: Grep A Pattern From File
Popular Question
2.2 years ago,
created a question with more than 1,000 views.
For LOD score of a single genotype
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
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3.5 years ago,
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For C: How to extract specific chromosome from vcf file
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For A: Trouble filtering CDS regions from Nextera Enrichment design
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For Free HiSeq X Ten human genome fastq test data
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4.6 years ago,
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For A: Trouble filtering CDS regions from Nextera Enrichment design
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