User: Bioinfonext

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Bioinfonext120
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Korea
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3 hours ago
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2 years, 2 months ago
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Posts by Bioinfonext

<prev • 267 results • page 1 of 27 • next >
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How to set BLASTMAT environment variable on HPC
... Hi, I got error while running OTU picking for ITS data. I am woking on HPC server. How I can set BLASTMAT environment variable? RuntimeError: BLAST cannot run if the BLASTMAT environment variable is not set. Usually, the BLASTMAT environment variable points to the NCBI data directory, whi ...
software error written 11 hours ago by Bioinfonext120
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(Closed) How to replace first column of file with another file first column
... Hi I am looking for Linux command to replace the first whole column of a file with another file first column. Thanks ...
next-gen written 14 days ago by Bioinfonext120
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Comment: C: qiime1 taxonomy assignment
... Thanks, it is resolved. by default, it used uclust method and I have provided rdp method. ...
written 18 days ago by Bioinfonext120
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qiime1 taxonomy assignment
... I need to ask one thing about `qiime1` for OTU assignment I used below command is it correct to use -m rdp when providing fasta and taxonomy file I assign OTU using this command: assign_taxonomy.py -i seqs.fna_rep_set.fasta –r 97_otus.fasta –t 97_otu_taxonomy.txt -m rdp I used fasta and taxonomy ...
next-gen written 18 days ago by Bioinfonext120
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Comment: C: Qiime2 manifest file for multiple pair end read
... manifest.csv giving out is like this: 6_S22_L001_R1_001.fastq.gz,,forward 6_S22_L001_R2_001.fastq.gz,,forward 7_S32_L001_R1_001.fastq.gz,,forward 7_S32_L001_R2_001.fastq.gz,,forward /mnt/scratch/users/3052771/Amplicon_data_july_2018/16S_Analysis/soil_16s//Soil_10_S52_R1_001 ...
written 25 days ago by Bioinfonext120
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Qiime2 manifest file for multiple pair end read
... Hi, I do have multiple pair end read file for amplicon sequencing, I am trying to make `bash` script` to generate manifest file: manifest file should contain information like this: > Blockquote *sample-id,filename,direction a,a_1_R1_001.fastq.gz,forward b,b_2_R1_001.fastq.gz,forward c,c_3_R ...
next-gen written 25 days ago by Bioinfonext120
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Comment: C: Qiime2 import command error
... Thanks Ram for this. ...
written 26 days ago by Bioinfonext120
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Qiime2 import command error
... I have loaded Qiime2 by calling module load on HPC: module load apps/qiime/2.0.1.20160711/bin When I type qiime info command: It shows below text [305@login2(ken) test_qiime2]$ qiime info System versions Python version: 3.5.2 QIIME version: 2.0.1.dev0 q2cli version: 0.0 ...
software error written 26 days ago by Bioinfonext120 • updated 26 days ago by RamRS20k
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importing data into Qiime2
... I am not able to understand how do we import data into Qiime2. Pair end reads do not contain barcode. In Qiime 1 we, just use split_libraries.fastq.py and we need as input: mapping txt file, sample ID and joined pair end reads for each sample, How do we perform this step in `QIIME2`: Do we need p ...
next-gen written 26 days ago by Bioinfonext120
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Comment: C: ITSx error on HPC
... Thanks, it is resolved with admin help. ...
written 26 days ago by Bioinfonext120

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