User: askif4

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askif40
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Posts by askif4

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Is there any good chromosome recombination(crossover) analysis tools that are not old?
... I have been searching for recombination analysis tools. (for mammalian genome data, not virus or bacteria) I think "ReCombine"(https://doi.org/10.1371/journal.pone.0025509) is the tool that is not that outdated, but there is no tutorial for the tool and it is very difficult to understand as a begin ...
gene assembly recombination sequencing written 7 weeks ago by askif40
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Questions using "WhatsHap" tool for haplotype phasing
... I have been using "WhatsHap"(https://whatshap.readthedocs.io/en/latest/index.html) tool for haplotype phasing. And it had been working very well. Actually, that is the problem. In the tutorial page, The basic command-line for running WhatsHap is this: whatshap phase -o phased.vcf --referen ...
haplotype snp phasing sequencing written 7 weeks ago by askif40
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Comment: C: How to check if a Fastq file is contaminated with other strains?
... This worked perfectly! Thank you again ...
written 8 weeks ago by askif40
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Comment: C: How to check if a Fastq file is contaminated with other strains?
... Thank you! I would try that tool ...
written 8 weeks ago by askif40
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Comment: C: How to check if a Fastq file is contaminated with other strains?
... Thank you for your reply, I will try ...
written 8 weeks ago by askif40
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Comment: C: How to check if a Fastq file is contaminated with other strains?
... Ah, I was searching for the mutation spots with low VAFs. And I found some suspicious reads. So I copied the read sequences and pasted them into web Blastn. That's how I found out that it was contaminated. It was like this https://ibb.co/5jD8qtV ...
written 8 weeks ago by askif40
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How to check if a Fastq file is contaminated with other strains?
... I have some Fastq files of the mouse(later mapped to the B6=mm10 reference sequence). But when I looked at bam files with IGV, some reads were found out to be Rat's (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.5) I have used web Blastn to check some of the reads but it is impossible to che ...
gene assembly next-gen sequencing written 8 weeks ago by askif40
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Comment: C: How to calculate VAF from BAM or SAM(+pileups) files using pysam?
... I already have the location of the mutations, which means I have VCF files from BAM files I know that there are other methods to calculate VAF(using VCF files), even if it is not efficient, I want to use pysam. Thanks~ ...
written 10 weeks ago by askif40
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How to calculate VAF from BAM or SAM(+pileups) files using pysam?
... I assume pysam is a tool for BAM, SAM file. But since the official document is a bit hard to understand. I am having difficulties calculating VAF values with pysam. If you could suggest to me some scripts or documents, it would be grateful. Thank you. (It would be better if the method is restric ...
bam vaf pysam snp sequencing written 10 weeks ago by askif40
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How to determine specific strains(mouse) from BAM(or VCF) by unknown sample? (using or not using dbSNPs)
... I have downloaded the mouse strain-specific VCF files(dbSNP) from Sanger institute. And I have my own VCF files of C57, Balb/C mouse. I want to compare my vcf files with Sanger VCF files in order to find which dbSNPs will match the most with my VCF files. I used '**vcf-compare**' from **vcftool ...
vcf mouse dbsnp snp written 11 weeks ago by askif40

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