User: xioli2013
xioli2013 • 10
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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 2.6 years ago by
xioli2013 • 10
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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 2.6 years ago by
xioli2013 • 10
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... 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 ...
written 2.6 years ago by
xioli2013 • 10
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... 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 ...
written 2.6 years ago by
xioli2013 • 10
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... 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 2.7 years ago by
xioli2013 • 10
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... 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 2.7 years ago by
xioli2013 • 10
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... 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 2.7 years ago by
xioli2013 • 10
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... Hi Kevin, I just added the links to the reads. Hope you can take a look at them.
...
written 2.7 years ago by
xioli2013 • 10
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... 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 ...
written 2.7 years ago by
xioli2013 • 10
• updated
2.7 years ago by
Kevin Blighe ♦ 63k
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... 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 2.7 years ago by
xioli2013 • 10
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