User: xioli2013
xioli2013 • 0
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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 3 months ago by
xioli2013 • 0
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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 3 months ago by
xioli2013 • 0
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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 3 months ago by
xioli2013 • 0
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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 4 months ago by
xioli2013 • 0
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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 4 months ago by
xioli2013 • 0
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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 4 months ago by
xioli2013 • 0
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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 4 months ago by
xioli2013 • 0
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... Hi Kevin, I just added the links to the reads. Hope you can take a look at them.
...
written 4 months ago by
xioli2013 • 0
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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 4 months ago by
xioli2013 • 0
• updated
4 months ago by
Kevin Blighe ♦ 16k
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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 5 months ago by
xioli2013 • 0
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