User: bataloffv

gravatar for bataloffv
bataloffv20
Reputation:
20
Status:
New User
Location:
Last seen:
2 months, 1 week ago
Joined:
3 months ago
Email:
b********@gmail.com

Posts by bataloffv

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
171
views
1
answers
Comment: C: Reads mapped with zero quality still mapped to exactly one position
... Thank you the answer. Looking at optional tags, I guess this is the indication of where the reads alternatively map? XA:Z:chr21,-6454604,150M,0; XA:Z:chr21,+6454616,150M,0; XA:Z:chr21,+6454627,150M,4; XA:Z:chr21,+6454627,150M,0; XA:Z:chr21,+6454627,150M,1; XA:Z:chr21,+645462 ...
written 11 weeks ago by bataloffv20
0
votes
1
answer
171
views
1
answers
Comment: C: Reads mapped with zero quality still mapped to exactly one position
... The output: 4 147 1 161 11 163 1 339 1 355 9 83 6 99 ...
written 11 weeks ago by bataloffv20
0
votes
1
answer
171
views
1
answers
Comment: C: Reads mapped with zero quality still mapped to exactly one position
... Bwa was piped after picard SamToFastq: picard SamToFastq \ I=markilluminaadapters.bam \ FASTQ=/dev/stdout \ CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=2 INTERLEAVE=true NON_PF=true | \ bwa mem -M -t 4 -p /path/to/broad/hg38.fasta /dev/stdin > algn.sam ...
written 11 weeks ago by bataloffv20
4
votes
1
answer
171
views
1
answer
Reads mapped with zero quality still mapped to exactly one position
... Hi everybody! I'm new to bioinformatics and to this forum. I have Illumina paired-end whole genome sequencing data (read length is 150bp) aligned with bwa. There are regions where all reads are mapped with zero quality. I took all reads covering a specific coordinate from such region: $ samtool ...
mq mapping quality mapq bwa written 11 weeks ago by bataloffv20 • updated 11 weeks ago by Istvan Albert ♦♦ 85k
1
vote
0
answers
229
views
0
answers
Comment: C: Make genes from GTF annotation searchable in IGV
... Thank you for the replies. I already tried increasing allowable memory (-Xmx12g instead of -Xmx4g in igv.sh). Still IGV demands the gtf to be indexed. With everything loaded (the gtf, a wgs bam, and a couple of vcfs) IGV uses just 1.6G of RAM. Actually, I already had found what I was looking for, at ...
written 12 weeks ago by bataloffv20
0
votes
0
answers
229
views
0
answers
Comment: C: Make genes from GTF annotation searchable in IGV
... I run it locally. Apparently, the reference genome that I use, has no annotation track. So, according to the user guide you that you provided the link to, I should use a non-indexed feature track to be able to search genes in it, and the feature track is too large to be loaded without indexing. ...
written 3 months ago by bataloffv20
2
votes
0
answers
229
views
0
answers
Make genes from GTF annotation searchable in IGV
... Hi everybody! Probably a basic question. I have a bam aligned against a hg38 reference from Broad Institute. I also have a gtf annotation file. Everything loads and displays in IGV, but the search isn't aware of gene names from the GTF file. Actually the only way to use the IGV search box is to type ...
gtf gene igv written 3 months ago by bataloffv20

Latest awards to bataloffv

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2335 users visited in the last hour