User: mirza

gravatar for mirza
mirza80
Reputation:
80
Status:
Trusted
Location:
India
Last seen:
10 months, 2 weeks ago
Joined:
3 years, 5 months ago
Email:
m***************@gmail.com

Posts by mirza

<prev • 174 results • page 1 of 18 • next >
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Help regarding variant filtration and variant density calculation
... I have completed variant calling and annotation and I need help with the following analysis. Is it possible to do the following analysis with my vcf files using vcftools or snpsift or bedtools? 1. Count the heterogygous SNPs according to different class i.e. C/T; T/C; etc 2. Calculate variant dens ...
bedtools variant filtration snpdensity vcftools written 20 months ago by mirza80
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Comment: C: How to draw circular plot to show genomewide snps and indels distribution?
... thank you all for your reply. ...
written 22 months ago by mirza80
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How to draw circular plot to show genomewide snps and indels distribution?
... Hi, I have 2 related fungal isolates and am working on variant calling. I have called variants using samtools-bcftools and have annotated them using snpEff. What tools can I use to draw a circular plot to represent snps and indels distribution? I want to generate a plot like this [Genome analysis ...
circular plot snp distribution written 22 months ago by mirza80
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Comment: C: Optical mapping service company or lab
... ok, thanks caizexi123. ...
written 22 months ago by mirza80
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Comment: C: Optical mapping service company or lab
... Hello Daniel, I am in New Delhi, India and working on fungal & bacterial NGS analysis. Is it possible for your team to provide a similar service to us? ...
written 22 months ago by mirza80
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Comment: C: Problem using picard reordersam
... thanks for the option, it worked. But, can you explain why is it highly dangerous ( & any related article or post you can direct me to)? ...
written 23 months ago by mirza80
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Comment: C: Problem using picard reordersam
... any command other than `cat myreference.fa` to view the reference coz' the reference has 2600 scaffolds! and I can see only the last few in my terminal. Anyhow, I am sure this is the same file. ...
written 23 months ago by mirza80
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Comment: C: Problem using picard reordersam
... I am using the same reference file that I used for mapping. ...
written 23 months ago by mirza80
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Problem using picard reordersam
... Hi, I am working on variant calling with a fungal genome. When I am trying to reorder my .bam file (sorted) using picard ReorderSam (picard v2.9.0) to be used further in GATK realignment & BQSR, it throws this error: Exception in thread "main" picard.PicardException: Discordant contig lengt ...
picard reordersam written 23 months ago by mirza80 • updated 23 months ago by Pierre Lindenbaum118k
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Comment: C: samtools variant calling workflow
... @Santosh Hi, GATK requires read group tag @RG. I have aligned my reads using bowie2 (without the use of RG tag, as I never required it earlier) and completed the 7 steps of my workflow. Now, I read that we can add RG using picard but the big question, what values I will give in the command? I have ...
written 23 months ago by mirza80

Latest awards to mirza

Popular Question 20 months ago, created a question with more than 1,000 views. For How to create gene-gene/ protein- protein interaction network using Cytoscape?
Popular Question 20 months ago, created a question with more than 1,000 views. For Mapping with tophat2 and setting a Tophat2 output directory?
Popular Question 20 months ago, created a question with more than 1,000 views. For VelvetOptimizer:Error in running the program
Popular Question 20 months ago, created a question with more than 1,000 views. For How can I upgrade bowtie2-2.2.6 to bowtie2-2.2.9 or uninstall this old version?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to add tophat and bowtie to the path?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to rename headers in fasta files keeping some fractions and adding a name?
Popular Question 20 months ago, created a question with more than 1,000 views. For samtools sort- no output file generated
Centurion 2.3 years ago, created 100 posts.
Supporter 2.6 years ago, voted at least 25 times.

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