User: deepti1rao

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deepti1rao0
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Posts by deepti1rao

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Comment: C: Removal of PCR dupliactes from trimmed reads
... Thanks! Got it! Why do I still have 14% duplicates? ...
written 23 hours ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... Thanks! Will try prinseq! ...
written 23 hours 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 23 hours 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 23 hours ago by deepti1rao0
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Comment: C: Removal of PCR dupliactes from trimmed reads
... How can I find this out? ...
written 23 hours 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 1 day 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 1 day ago by deepti1rao0
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Removal of PCR dupliactes from trimmed reads
... I have tried samtools rmdup on my paired end fastq files, which were earlier trimmed. According to the samtools manual, rmdup works as follows: Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. I have 23% ...
duplicates samtools rmdup pre-processed reads written 1 day ago by deepti1rao0 • updated 1 day ago by genomax32k
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Comment: C: Does Bowtie2 Map Multiple Reads To The Same Gene?
... And then how do you go about deciding which read is the best match if mapQ is also the same for all? ...
written 8 days ago by deepti1rao0
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Aligner to work with PAN genomes and short reads
... Is it possible to align short reads to a PAN Genome? Which aligner can be used for this purpose? ...
genome aligner pan written 10 days ago by deepti1rao0

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