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Search: Posts Made By: Maulik23
Forum: Bioinformatics 08-24-2013, 09:08 PM
Replies: 1
Views: 2,402
Posted By Maulik23
mulitple/split/chimeric reads from bwa bwasw long read aligner and SNP calling

I have some queries about split /chimeric reads: 1) Though I have read several defintions of split reads as given in this thread: http://seqanswers.com/forums/showthread.php?t=2267. I am stil unable...
Forum: Bioinformatics 01-20-2013, 02:35 AM
Replies: 0
Views: 841
Posted By Maulik23
chimeric reads from BWASW

Should I be worried about chimeric reads after performing reference guided assembly using bwasw??? I aimed to detect SNP from exome sequencing data of buffalo genome :confused:
Forum: Bioinformatics 01-20-2013, 01:14 AM
Replies: 1
Views: 1,192
Posted By Maulik23
Difference between Multiple hits and Chimeric hits

what is the difference between chimeric hits and multiple hits? Does chimeric hits affects the SNP detection in further downstream analysis? If the answer is positive then can any1 suggest me the...
Forum: Bioinformatics 12-25-2012, 08:24 AM
Replies: 2
Views: 1,728
Posted By Maulik23
thanks for reply :) but my concern is with 454...

thanks for reply :) but my concern is with 454 sequencing data because I have not came across any good reference which has used GATK for SNP calling from Roche 454 sequencing data. Can you please...
Forum: Bioinformatics 12-24-2012, 07:41 PM
Replies: 2
Views: 1,728
Posted By Maulik23
GATK pipeline for SNP calling from 454 GS-FLX sequencing data????

I want to call SNPs in GATK using the BAM file produced by GS Reference mapper , bu the problem with BAM file is it does not contain the read group so how to add read group in the bam file of 454...
Forum: Bioinformatics 12-23-2012, 09:21 PM
Replies: 1
Views: 1,378
Posted By Maulik23
Add read groups in .bam file from 454 sequencing

how to add read groups in BAM file of 454 sequencing data using PICARD for further downstream processing in GATK?:confused:
Forum: Bioinformatics 09-23-2012, 04:47 AM
Replies: 2
Views: 1,239
Posted By Maulik23
Comparison of SNPs between case and control sample

I want to compare the SNPs between case and control groups. Which software should I use?
Any help will be appreciated :)
Forum: Bioinformatics 09-11-2012, 09:09 AM
Replies: 1
Views: 989
Posted By Maulik23
extract the positions from genome where reads from all the samples have aligned

I have aligned 454 reads from 8 different individuals to the human reference genome using GS reference mapper and converted this alignment into BAMfile now how can I extract the genome positions...
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