User: kshitijtayal

gravatar for kshitijtayal
kshitijtayal30
Reputation:
30
Status:
New User
Location:
India
Last seen:
2 years, 6 months ago
Joined:
3 years, 6 months ago
Email:
k***********@gmail.com

Posts by kshitijtayal

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Aligning using Bowtie2
... @Carambakaracho Max value that i can set for N is 1. Is there any other possible way ? Description for -N - Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sen ...
written 2.5 years ago by kshitijtayal30
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Aligning using Bowtie2
... I am using Bowtie2 to align the reads to lambda_virus genome using the following command. ./bowtie2 -x lambda_virus -U example/reads/reads_1.fq -S eg1.sam It shows following output in the console i.e. 10000 reads; of these: 10000 (100.00%) were unpaired; of these: 596 (5.96%) a ...
bowtie2 forum alignment written 2.5 years ago by kshitijtayal30 • updated 2.5 years ago by Carambakaracho930
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Obtaining phased haplotype data
... Hi all, I am doing my research on Haplotype inferencing and i need my hand on some real phased haplotypes. I understanding that haplotype data is available at international [Hap-Map project][1] but the problem is that it comes from a tool called Shapeit. Can anybody point me to any resource where ...
next-gen haplotype sequencing written 3.1 years ago by kshitijtayal30 • updated 6 months ago by RamRS20k
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Obtaining fastPHASE tool
... Over the year PHASE tool has been considered as a gold standard for Haplotype inference. But the problem with the tool is that it is very slow to work it. They developed another tool called fastPHASE which is supposed to be fast as compared to PHASE tool. But unfortunately it is nowhere available in ...
haplotype next-gen phase written 3.2 years ago by kshitijtayal30 • updated 18 months ago by Gennady Khvorykh90
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Speed up PHASE software for haplotype inference
... I am a Bioinformatician and recently stuck in a problem which requires some scripting to speed up my process. We have a software called PHASE and Command that i type in my command line to fire software is     ./PHASE test.inp test.out where PHASE is the name of the program and test.ip is the input ...
multithreading haplotype unix written 3.2 years ago by kshitijtayal30
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Comment: C: understanding wgsim flags
... i don't know about the real data but synthetic reads do come with fixed read length. Assuming read length and fragment length are the same , again my question would be what is the role of standard deviation in generating synthetic reads ? ...
written 3.4 years ago by kshitijtayal30
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understanding wgsim flags
... I am listing below various flags that are used by wgsim. Wgsim simulate sequence reads from a reference genome . -e FLOAT base error rate [0.020] -d INT outer distance between the two ends [500] -s INT standard deviation [50] -N INT number of read pairs [1000000] -1 INT length of the first read ...
alignment sequencing written 3.4 years ago by kshitijtayal30 • updated 3.4 years ago by Devon Ryan88k
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Comment: C: Existing Tools For Viewing A De Bruijn Graph From Raw Reads
... Thank you for introducing me to this great tool. It would be of great help. However i have a doubt of mine that i would like to clarify . Bandage only supports loading assembled graph only. If i have a read file and want to view De briujn graph directly, it is impossible using Bandage. For bandage y ...
written 3.4 years ago by kshitijtayal30
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Existing Tools For Viewing A De Bruijn Graph From Raw Reads
... I understand that there are plethora of tools available where you enter the read file and the software will internally build the De bruijn graph and will display the assembled genome. I want to actually see the debruijn graph that has been constructed from the read file. Is there any tool available ...
genome assembly next-gen written 3.4 years ago by kshitijtayal30 • updated 3.4 years ago by h.mon24k
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Comment: C: How to handle Reverse complement in De-Bruijn Graph
... Many thanks for the prompt reply. After reading your reply , one more question arises in mind that if every graph node has two values then which value to take in case of Eulerian walk ? I was wondering if there are any existing tools for viewing a de Bruijn graph from raw reads? ...
written 3.4 years ago by kshitijtayal30

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