User: gtasource
gtasource • 30
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Posts by gtasource
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... I'm looking to use the custom env_nt database for Kraken2, but it's taking forever to mask the file. Does anybody have an already masked env_nt database file I can download directly to speed up this process? Thanks! ...
written 17 days ago by
gtasource • 30
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... Just to clarify, the * in the chromosome signifies unmapped reads? So, in the above command, since I am extracting unmapped reads into a separate file, that file should have mostly reads with * in the chr field. ...
written 21 days ago by
gtasource • 30
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... I know, this question is everywhere. But I have yet to see somebody use the same samotols command as myself, and I wanted to double-check.
samtools view -S -f 4 aligned.sam > unmapped.sam
Yay?
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... Hi all,
We have some metagenomic shotgunning data that we assembled into contigs using SOAPdenovo. Now, we wanted to feed these contigs into Kraken2. However, I've looked over some literature, and it seems like most people feed the raw reads into Kraken2. Is there any advantage using contigs? O ...
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... The FASTQ file that is giving the errors was generated from Kneaddata to remove human data from the dataset (we are doing a metagenomics analysis.) When uploading the original FASTQ file, no header issues are given.
I don't have to use Kneaddata for removal of the human contamination using a ref ...
written 7 weeks ago by
gtasource • 30
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... Illumnia Base Space is giving me this error that my FASTQ files have inconsistent header information.
This file contains inconsistent header information. We expected all cluster headers to match `'@Sample:116:FlowId:1:1101:19361:1047:N:0:AGTCAACA+TCTTTCCC#0/1'`
but we encountered the header `'@Sam ...
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... I have metagenome shotgunning data that I am running through metaphlan2. As per advice from other posts, I made sure to remove human contamination using kneaddata and trimmed based upon kit recommendations. However, the issue is removing the human data yields no results whatsoever from metaphlan2 ...
written 7 weeks ago by
gtasource • 30
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... We have some metagenomics shotgunning data we are looking to analyze with metaphlan2. Looking at the biobakery pipeline, they have you use kneaddata for trimming and removal of human contaminants, before moving on to the actual analysis. My question is, how much of a necessity is it to remove thes ...
written 7 weeks ago by
gtasource • 30
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... Thanks! That's exactly what I was looking for. Cheers! :) ...
written 7 weeks ago by
gtasource • 30
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... I'm looking to use FASTX to trim off 15 bases at 3’ end of read 1 and 15 bases at 5’ of read 2. But when I look at the FASTX command, it's not entirely clear to me on how to go about it. The two options that would be used are:
[-f N] = First base to keep. Default is 1 (=first base).
...
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