User: Agaz Hussain Wani

Reputation:
40
Status:
New User
Location:
India
Last seen:
1 month, 3 weeks ago
Joined:
3 years, 7 months ago
Email:
h************@gmail.com

Posts by Agaz Hussain Wani

<prev • 45 results • page 1 of 5 • next >
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Comment: C: bowtie options for exact match with reference short sequence
... How to tell your tool to extract only the exact matching reads. I have asked the question https://www.biostars.org/p/334795/#335724 ...
written 11 weeks ago by Agaz Hussain Wani40
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Comment: C: Count exact match reads in SAM file
... Thank you for your comment. I tried using `BBMap` and I used the command `reformat.sh in=output.sam out=exact.fastq`, however, I am not able to find how to extract exact matching reads. The given command extracts all the reads to the new file. ...
written 11 weeks ago by Agaz Hussain Wani40
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Count exact match reads in SAM file
... I got the alignment result in SAM format using bowtie2. As bowtie2 does not have the setting for exact match, so I want to count the number of exact match. I tried to use `grep` to extract the exact reads using `grep AS:i:0 old.sam >> newfiltered.sam` and when I try to count by `samtools` u ...
exactmatch alignment sam written 12 weeks ago by Agaz Hussain Wani40
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Comment: C: How to interepet wgsim roc results
... I found a very informative post here http://research.cs.wisc.edu/wham/comparison-using-wgsim/, still comments are welcome. ...
written 8 months ago by Agaz Hussain Wani40
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How to interepet wgsim roc results
... I am trying to get the roc results for various tools by using `wgsim` tool which I at http://lh3lh3.users.sourceforge.net/alnROC.shtml. I tried the following command `wgsim_eval.pl alneval -ag50 results.sam > results.roc ` and I got something like `255 51557 3890`, sometimes `255 3624 1190`. I ...
next-gen alignment roc wgsim written 8 months ago by Agaz Hussain Wani40
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Comment: C: What is each sequence valid identifier
... Great!, thank you very much. ...
written 11 months ago by Agaz Hussain Wani40
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Comment: C: What is each sequence valid identifier
... Thank you, it seems alright when I open the files in text mode, display on ssh terminal is different. ...
written 11 months ago by Agaz Hussain Wani40
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Comment: C: What is each sequence valid identifier
... Thank you, after doing `fastq-dump --split-3 SRR3620050` I got the file split into `SRR3620050_1.fastq` and `SRR3620050_2.fastq`, but still a read is split on more than 4 lines. ...
written 11 months ago by Agaz Hussain Wani40
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Comment: C: What is each sequence valid identifier
... Sorry for coming back. As I understood that fastq files follow a 4 line standard. But while downloading sequence data I came across samples with read length 600 (SRR3620050) and 400 (SRR5419561), which are spread on more than 4 lines, and the data is made public recently. I downloaded that data by ...
written 11 months ago by Agaz Hussain Wani40
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Where can I get fastq sequence files of length 150 and more.
... I want to perform alignment of the human sequence reads with the reference genome. I need reads length 150 and more (500) to test some algorithm. Where can I find such type of reads, both single and paired-end. I got reads from [1000 genome project](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/ ...
alignment sequence written 11 months ago by Agaz Hussain Wani40 • updated 11 months ago by Vijay Lakhujani3.2k

Latest awards to Agaz Hussain Wani

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