User: christina

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christina0
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Posts by christina

<prev • 5 results • page 1 of 1 • next >
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metaphlan2 --biom option error
... Hi, I am trying to use the --biom option for running a metaphlan2 run with the intermediate bowtie2.bz2 files from a previous run. Command to run metaphlan2: python /home/user/metaphlan2/metaphlan2.py sample.bowtie2.bz2 --nproc 12 --input_type bowt ie2out --biom sample.biom > samp ...
metaphlan2 metagenomics biom biom format written 11 months ago by christina0
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OBItools - obisilva - expected output files?
... Hi, I have been using obitools for my analysis of 16S metabarcoding data. Just trying to create an ecoPCR database from the SILVA SSU database, prior to taxonomic assignment. As per the manual, I have tried the following: obisilva --ssu --parc --local=/home/silva_db the folder silva_db conta ...
metabarcoding obitools obisilva written 11 months ago by christina0
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Comment: C: blast against metagenome shotgun data - not getting the hits expected
... Thanks for your reply. I had decided to do it this way around, simply because it is less computationally intensive. But I have since tried the reverse and that is working. I am still puzzled by the behaviour though. I tried some other samples and for those I got results that were concordant between ...
written 19 months ago by christina0
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Comment: C: blast against metagenome shotgun data - not getting the hits expected
... I downloaded paired raw read fastq files from the SRA archive. Converted to fasta using: cat sampleA_R1.fastq | paste - - - - | cut -f 1,2 | sed 's/^@/>/' | tr "\t" "\n" > sampleA_R1.fasta combine both runs using cat sampleA_R1.fasta sampleA_R2.fasta > sampleA.fasta then cr ...
written 19 months ago by christina0
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blast against metagenome shotgun data - not getting the hits expected
... Hi all, I am currently performing blast searches for a species of interest by blasting a genome assembly against custom databases of metagenome shotgun data. Everything seems to be working fine and I am getting hits, if I create a database from a single sample (i.e. paired reads, converted fastq t ...
metagenomics blast written 19 months ago by christina0 • updated 19 months ago by 5heikki8.9k

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