User: jigarnt
jigarnt • 30
- Reputation:
- 30
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- New User
- Location:
- Canada
- Last seen:
- 2 years, 3 months ago
- Joined:
- 3 years, 6 months ago
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Posts by jigarnt
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... Hi All Bioinformaticians,
I want to generate a 'LD heatmap' which depicts the decay in LD in the portions of genome where recombination has occured. For the same, I am using VCFtools to calculate LD. However, my doubt is, Does the script work for a haploid organism?
Is the '--hap-r2' argument in ...
written 2.4 years ago by
jigarnt • 30
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... Hi Devon,
Many thanks for having a look at it. I tried with those numbers before, but got the same error. Is there any other way, to get the base pair information at each positions in your BAM files? ...
written 2.6 years ago by
jigarnt • 30
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... Hi Devon,
In the file, it is actually supercont1.1. and not Supercont1.1. Would you mind having a look at the fasta file? It is available at the NCBI. It is an 30mb file so would not consume much time of yours. Organisms name is Geomyces destructans ...
written 2.6 years ago by
jigarnt • 30
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... Hi Devon,
Thank you for your response. I tried your suggestion of indicating the chromosome positions but it is giving me the same error:
/Users/lindakohn/Desktop/Tools/samtools-1.3/samtools mpileup -f GCF_000184105.1_Geom_destructans_V1_genomic.fa -r supercont1.1:1-1847 712206_realigned_reads.bam ...
written 2.6 years ago by
jigarnt • 30
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... Hi All,
I intend to know the base frequencies at each positions in my BAM files. For the same, I am using samtools mpileup script, which can serve the purpose. While running the script, I am encountering an error which is not understandable by me. So I am reaching out to all the expert bioinformat ...
written 2.6 years ago by
jigarnt • 30
• updated
2.6 years ago by
Devon Ryan ♦ 88k
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... Hi All,
I am thinking of using Mpileup from Samtools to get the information on the read quality and read depth from the BAM files. In that case which script should I use?
I have been recommended the script below:
ref=my_fasta.fasta
samtools mpileup -f $ref -r chromosome_1:1018000-1018100 my_bam. ...
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... Hi Venu,
Thanks for your response. I also ran this script in linux but I am getting the same error. I suspect there is an issue with the script.
Whats your take? ...
written 2.8 years ago by
jigarnt • 30
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... Hi All,
I am trying to run this custom perl script available on GIThub for detecting recombination through Four-gamete test. As this is my first hands on Perl, I am not able to figure out where I am going wrong. Although I know the basic do's and dont's of a running scripts on command prompt/termin ...
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Comment:
C: Tajima's D value interpretation
... I have calculated Tajima's d from Pairwise data and no of segregating sites. How to Normalize "d" valus into "D" manually as I have calculated my Tajima's d from character data and not sequence data. ...
written 2.9 years ago by
jigarnt • 30
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... Hi,
The chances of contamination are highly unlikely because it showed up as a distinct band everytime I isolated the DNA from the same sample but different isolates grown in different plates. It was after its occurence everytime we decided to illumina sequence it. Our first guess was that it is a p ...
written 3.0 years ago by
jigarnt • 30
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For Finding True SNPs after hard filtering on GATK
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