User: nadiabeg.comsats

Reputation:
0
Status:
New User
Last seen:
1 day, 7 hours ago
Joined:
2 months, 1 week ago
Email:
n***************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by nadiabeg.comsats

<prev • 9 results • page 1 of 1 • next >
0
votes
0
answers
56
views
0
answers
10x genomics linked reads-- preprocessing
... Hi everyone, I have aligned reads using long ranger. Then I have removed supplementary, duplicated reads using samtools. Is it necessary to use picard tools after alignment to mark duplicates if they are aligned using longranger? Or longranger does it automatically? ...
alignment 10x genomics written 17 days ago by nadiabeg.comsats0
0
votes
0
answers
476
views
0
answers
Comment: C: Using freebayes to call variants
... -p is basically the ploidy. you have mentioned -p 48 means your samples have 48 genome copies. see this link for detailed explanation: https://github.com/ekg/freebayes ...
written 20 days ago by nadiabeg.comsats0
0
votes
1
answer
64
views
1
answers
Comment: C: Variant using freebayes
... Why not just start with 1/1/1/1 and 0/0/1/1 to find something more definitive and less enriched for false positives ? sorry I am not getting your this point. In my results I have SNPs with GT tag :0/1/1/1, few with tag:0/0/0/1, 0/0/0/0, 0/0/1/1. As I am dealing tetraploid specie for the first time ...
written 27 days ago by nadiabeg.comsats0
0
votes
1
answer
116
views
1
answers
Comment: C: Getting uniquely aligned properly paired reads
... Yes it uses both but the parameters are tuned according to diploid genome. In my case I have tetraploid samples. ...
written 27 days ago by nadiabeg.comsats0
1
vote
1
answer
64
views
1
answer
Variant using freebayes
... Hi all, I have 10x genomics data for tetraploid (4n) plant specie. I am using following script for the variant calling. $free_bayes -f $ref -p 4 $bam >semlo.vcf I have set ploidy to 4. Is this a correct way of variant calling for tetraploid genomes. In my results I am getting genotype tag (GT ...
tetraploid genome freebayes 10x genomics written 27 days ago by nadiabeg.comsats0 • updated 27 days ago by colindaven1.9k
0
votes
1
answer
116
views
1
answers
Comment: A: Getting uniquely aligned properly paired reads
... You mean something is wrong with the 10x genomics sequenced file or with the alignment file? Sure I will try that. ...
written 29 days ago by nadiabeg.comsats0
0
votes
1
answer
116
views
1
answers
Comment: C: Getting uniquely aligned properly paired reads
... Yes I am using longranger for alignment. Well I am only aligning the reads using -- longranger align parameter so I am not getting any vcf file out of it. But before getting VCF,I want to filter the bam file. Then pre-processing bam file --local realignment using GATK --- variant calling using free ...
written 29 days ago by nadiabeg.comsats0
1
vote
1
answer
116
views
1
answer
Getting uniquely aligned properly paired reads
... Hi all, I have bam files obtained from mapping 10x genomics data. My goal is to get the VCF file. To do the variant calling I want to get rid of the unaligned, multi mapping and other cases. Goal is to get uniquely aligned properly paired reads. My initial statistics of mapping are (without filter ...
1
vote
1
answer
88
views
1
answer
Trimmomatics_ loading module error
... Hi I have downloaded trimmomatic version 0.39. I am trying to use it using module load trimmomatic. The problem is each time I get an error message: Unable to locate a modulefile for 'Trimmomatic-0.39/' This software is a Java executable .jar file; thus, it is not possible to add to the PATH envir ...
trimmomatic-0.39 written 10 weeks ago by nadiabeg.comsats0 • updated 10 weeks ago by lieven.sterck6.4k

Latest awards to nadiabeg.comsats

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: 1366 users visited in the last hour