User: gtasource
gtasource • 30
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Posts by gtasource
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... Hey guys,
I know that for a lot of people, looking at the market genes of a cluster is something that is done manually. Obviously, if you know a lot about the tissue you are dealing with, it’ll be easier to say that these marker genes are indicative of this cell type. But what if you have no idea ...
written 10 weeks ago by
gtasource • 30
• updated
10 weeks ago by
Kevin Blighe ♦ 54k
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... For any sort of single cell program, a big step is picking the amount of principal components for downstream analysis. However, the one approach that does not make sense is when people say to use heat maps. For starters, what exactly are we looking for when we analyze our heatmaps for, let’s say 5 ...
written 11 weeks ago by
gtasource • 30
• updated
11 weeks ago by
Kevin Blighe ♦ 54k
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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 3 months 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 3 months 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 4 months 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 4 months 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 4 months ago by
gtasource • 30
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