User: hua.peng1314

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hua.peng131490
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Posts by hua.peng1314

<prev • 33 results • page 1 of 4 • next >
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(Closed) Any treatment or drugs for menkes diseqses
... Hi,all,Maybe ask this question here is not a good choice,but I don't know where I can get some help. One of my friend told me her three months old son is diagnosed to have menkes disease.The boy have mutation c.3801G>C(E19 chrX:77296231 ATP7A).Copper Histidine may help him, but it is a kind of un ...
menkes written 3.4 years ago by hua.peng131490
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Answer: A: A question about preparing file for lefse
... Doctor Francesco Asnicar from has already sent my email.I will show it below. the problem with the Gp10 genus is that it is a candidate genus and species. According to the NCBI (http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=981385&lvl=3&keep=1&srchmode=1&u ...
written 3.6 years ago by hua.peng131490
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A question about preparing file for lefse
... Hi all.I used RDP database to classify my 16S sequence.It has some categories like this: Lineage=Root;rootrank;Bacteria;domain;"Acidobacteria";phylum;Acidobacteria_Gp10;class;Gp10;genus I don't think "k__Bacteria|p__Acidobacteria|c__Acidobacteria_Gp10|||g__Gp10" or "k__Bacteria|p__Acidobacteria|c__ ...
lefse written 3.6 years ago by hua.peng131490 • updated 2.5 years ago by Biostar ♦♦ 20
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The choise of the blast result for taxonomy assign
... Hi,I am dealing with some nifH gene. I translated the sequence into protein sequences and cluster them at 92% similarity. A part of result of BLASTp of the representative sequences is shown below.   Query id, Subject id, % identity, alignment length, OTU_64;size=38;    gi|563439003|gb|AHB60519.1 ...
taxonomy assign written 4.2 years ago by hua.peng131490
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Answer: A: the normal range of the percent of the singleton in UPARSE program
... The right quality of the read1 is: 200-204 23.87 28.2 9.8 36.8 2 38 205-209 23.65 29.2 8.8 36.4 2 38 210-214 21.20 24.2 2 35 2 37.6 215-219 20.24 22.8 2 34.6 2 37.2 220-224 19.33 ...
written 4.3 years ago by hua.peng131490
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Answer: A: the normal range of the percent of the singleton in UPARSE program
... Sorry I made some mistake. The title of the quality  should be lake this: #Base   Mean    Median  Lower Quartile  Upper Quartile  10th Percentile 90th Percentile ...
written 4.3 years ago by hua.peng131490
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the normal range of the percent of the singleton in UPARSE program
... Hi,all.I am dealing with some 16S rRNA data from Miseq platform.They are 2*300 reads. I use Flash software to merge them with the paramater -M 220 directly.And UPARSE is used to filter the low quality reads with the paramater -maxee 1. Here is the quality of one of the sample: read1: # ...
singleton 16s uparse written 4.3 years ago by hua.peng131490 • updated 4.3 years ago by 5heikki8.5k
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Answer: A: Confused about the quality control strategy of 16s pair_end sequence from Illumi
... My samples are collected from potting soil. I also think it looks really suspicious. I combining QIIME and mothur pipelines for mothur is hard to deal with so many reads. Here is what I did: flash -M 300 R1.fastq R2.fastq less out.extendedFrags.fastq|/fastx/fastx_barcode_splitter.pl --bcfile for ...
written 4.7 years ago by hua.peng131490
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Answer: A: Confused about the quality control strategy of 16s pair_end sequence from Illumi
... Thanks for your patient and friendly. I add answer but not reply because I can't click the "ADD REPLY" button.Maybe I am stupid to have ignored something. Trimming is not necessary for me.I just want to do something to make the OTUs to be generated correctly.  After merging with FLASH(default para ...
written 4.7 years ago by hua.peng131490
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Answer: A: Confused about the quality control strategy of 16s pair_end sequence from Illumi
... BBDuk is really an excellent work. But as the reads with lower quality bases at the end. After merging the lowest quality region would be in the middle of the merged reads.No matter what kind of sliding window would probably  cut the reads at the middle of the reads. So  merging will be less signif ...
written 4.7 years ago by hua.peng131490

Latest awards to hua.peng1314

Popular Question 3.6 years ago, created a question with more than 1,000 views. For The Utr Sequence Used To Predicted Mirna Target
Popular Question 4.2 years ago, created a question with more than 1,000 views. For quality control with the 16s miseq data
Popular Question 4.2 years ago, created a question with more than 1,000 views. For The Result Of The Mirdeep2
Popular Question 4.7 years ago, created a question with more than 1,000 views. For The Result Of The Mirdeep2

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