User: xioli2013

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xioli20130
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Posts by xioli2013

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Comment: C: How to map taxonomy to OTUs
... Thanks for the reply. I am using trnL as described in the question. I have solved the issue now. ...
written 6 months ago by xioli20130
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Answer: A: How to map taxonomy to OTUs
... I have solved the issue by creating right formatted id_to_taxonomy table and fed it to assign_taxonomy.py in QIIMME, which worked. ...
written 6 months ago by xioli20130
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How to map taxonomy to OTUs
... Hi, I have encountered an issue that I was trying to map taxonomy to an otu table. The barcode is trnL. I have managed to get all viridiplantae trnL sequences from NCBI as a database for local blast, and the associated lineage to each sequence entry. Also I have the representative sequences by vsea ...
otu trnl taxonomy table written 6 months ago by xioli20130
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formatting lineage to taxonomy file
... Hi, I am trying to make a taxonomy file like the one provided in qiime for all trnL gene. What I have done: 1. all trnL sequences 2. all trnL gene accession number 3. all trnL gene tax id I was able to get the lineage tag from the xml efetch function generated in Python: ``'1435590': 'cellular or ...
metabarcode taxonomy file formatting trnl written 7 months ago by xioli20130
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Comment: C: a confusion about pandaseq assembly
... Hi Kevin, thanks for the reply. One more question: Should the output of pandaseq assembly look like [forward primer][sequence][reverse primer] without trimming the primers? ...
written 7 months ago by xioli20130
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Comment: C: a confusion about pandaseq assembly
... Hi Kevin, here are the fastqc report, the quality of 3' is not good as it normally is for NGS [Foward QC][1] [Reverse QC][2] [1]: https://drive.google.com/open?id=1wee8D9nv_uiX8piqvBI0iLIBtHSIg9_a [2]: https://drive.google.com/open?id=19_srd3Z7gi5Z6mKiWGScXFTbz9n4IMXj What do you think woul ...
written 7 months ago by xioli20130
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Comment: C: a confusion about pandaseq assembly
... I played around the tools such as bbmerge and pandaseq with trimming and no trimming with trimmomatic 0.36 the # of raw reads in R1 is 194543 No trimming: ``$BBMerge in1=V1_R1.fastq in2=V1_R2.fastq out=bbmap_notrim_merged.fq outu=bbmap_notrim_unmerged.fq \`` ``adapters=NexteraPE-PE.fa ihist=ihist_ ...
written 7 months ago by xioli20130
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Comment: C: a confusion about pandaseq assembly
... Hi Kevin, I just added the links to the reads. Hope you can take a look at them. ...
written 7 months ago by xioli20130
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a confusion about pandaseq assembly
... Hi, I have a Miseq data with about 300 bp long, paired end reads, barcode is trnL(c)/UAA(h) The first step I am attempting is use pandaseq to assemble the pe reads this is the command line: ``pandaseq -f lane1-s001-indexN716-B-S502-B-ACTCGCTA-CTCTCTAT-V-1_S1 _L001_R1_001.fastq -r lane1-s001-index ...
pandaseq miseq written 7 months ago by xioli20130 • updated 7 months ago by Kevin Blighe24k
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Comment: C: Error when running Mothur MiSeqSOP: "Mock is not a valid group, and will be disr
... Have you solved the problem yet? I have encountered the exact same issue. I found out that the problem should be from the output of make.file command where it does not add the names of samples to the file. ...
written 8 months ago by xioli20130

Latest awards to xioli2013

Scholar 6 months ago, created an answer that has been accepted. For A: How to map taxonomy to OTUs

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