User: ankit4035hinsu

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Posts by ankit4035hinsu

<prev • 6 results • page 1 of 1 • next >
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Comment: C: SNP calling using samtools
... Thanks for the algorithms. Also, I will refrain from cross-posting on other site. ...
written 5 weeks ago by ankit4035hinsu10
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SNP calling using samtools
... Hi all, I have RNA-seq paired-end data from Illumina and I am using BWA-mem for mapping and samtools for SNP calling. I wanted to understand and get your opinion regarding following. 1. [B]What is the criteria for calling the variant[/B]? Specifically, at a particular position, how many reads shou ...
rnaseq samtools bcftools snp mpileup written 5 weeks ago by ankit4035hinsu10 • updated 24 days ago by Biostar ♦♦ 20
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Answer: A: Pick De Novo OTUs Qiime
... Hi, I think that by this time, you might have received solution to your problem. Nevertheless, here is the solution. * QIIME1 requires input file in proper way (called QIIME-compatible format). Their tutorial "454 tutorial for de novo OTU picking" has a demultiplexing step. This step does three th ...
written 12 weeks ago by ankit4035hinsu10
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Comment: C: Extract DNA sequence based on a single coordinate
... Although this is an easier method, one thing to take care is the co-ordinates. If you have given co-ordinates as 1 to 10 for extraction, your final sequence will have 9 nucleotides only. It will miss the first one (the same has been also shown in their example). It took me some time to figure this ...
written 12 months ago by ankit4035hinsu10
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Comment: C: Extracting paired-end reads from assembly file
... That is what I wanted....Thanks a lot.. ...
written 2.8 years ago by ankit4035hinsu10
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Extracting paired-end reads from assembly file
... Hi, I have two paired-end read files. I made a combined de novo assembly of both in CLC and it gave me around 150,000 contigs. Out of all this, I want to extract reads constituting some 200 contigs. What is the best approach for doing so? Thank you in advance! ...
assembly written 2.8 years ago by ankit4035hinsu10 • updated 14 months ago by Biostar ♦♦ 20

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