User: deepti1rao

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deepti1rao0
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Posts by deepti1rao

<prev • 28 results • page 1 of 3 • next >
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Consensus fasta file with uncovered bases set to Ns
... I am looking forward to generating a consensus fasta file by providing my BED file and the reference fasta as inputs.I want to have the bases in my reference genome, showing 0 coverage to be substituted by Ns. Is there any script/tool available to do this? ...
genome bed consensus reference fasta written 7 weeks ago by deepti1rao0 • updated 7 weeks ago by Matt Shirley7.9k
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Comment: C: Preprocessing the genomic data
... With no over represented sequences and no adapters showing up in the fastqc report, am I good to go? Or do I still need to check for adapters? ...
written 7 weeks ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... I'm worried about bias owing to duplicates, during variant calling. ...
written 7 weeks ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... Thanks! Got it! Why do I still have 14% duplicates? ...
written 8 weeks ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... Thanks! Will try prinseq! ...
written 8 weeks ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... I'm aware that there are some tools,which remove duplicates from reads, without the need to align them. But, I dont understand how these can make out the difference between a PCR duplicate and a repeat in the genome. ...
written 8 weeks ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... I used bbduk from bbtools to trim my reads. Yes, I lost some reads in the process of doing so, but not many. ...
written 8 weeks ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... How can I find this out? ...
written 8 weeks ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... "external coordinates" means both 5' as well as 3', doesn't it? ...
written 8 weeks ago by deepti1rao0
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Comment: A: Removal of PCR dupliactes from trimmed reads
... Also, I had 23% duplicates earlier. After using rmdup, I'm still left with 14% duplicates. ...
written 8 weeks ago by deepti1rao0

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