User: life99945

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life999450
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Posts by life99945

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Length of the amplicon after trimming
... Hi! I have illumina myseq 16s rRNA amplicon reads 300bp length with 17 bp primer. After trimming length of this amplicon must be 283 bp max. BBDuk says that out of 300k sequences 298k were trimmed. Some sequences length is bigger that 283 bp. I wonder what these sequences are? Some sequences hav ...
trimming written 6 months ago by life999450
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Visualyzing an otu table
... Hi! I was given an otu table in excel .xlsx format. I'm trying to visualyze it somehow, but i can't import it to qiime through "biom convert" maybe because of some sort of symbol corruptions. I also have 6 txt files "l2 phylum.txt; l3 class.txt; l4 order.txt; l5 family.txt; l6 genus.txt; l7 specie ...
excel otu table written 7 months ago by life999450 • updated 7 months ago by jrj.healey12k
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Comment: C: Removing primers with degenerate codes
... Thank you very much, everything worked out, but I do not understand why in the example they don’t use copyundefined? After all, it greatly affects the reverse read trimming. And how can i count minlength? In example they say that "min and max length were based roughly on 10% smaller and bigger than ...
written 8 months ago by life999450
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Comment: C: Removing primers with degenerate codes
... Thank you very much! ...
written 8 months ago by life999450
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Removing primers with degenerate codes
... Hello! I have forward and reverse illumina myseq 16s rRNA v4-v6 amplicon reads with Pro-mod-341F 5’-CCTAYGGGDBGCWSCAG and Pro-mod-805R 5’-GACTACNVGGGTMTCTAATCC primers used. I want to make sure these primers are already removed. Is there any way to do it? Thank you. ...
primers written 8 months ago by life999450 • updated 8 months ago by h.mon26k
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Comment: C: what read should i use for classifying?
... Thank you for the answer! I'v got this extended file from laboratory along with forward and reverse reads, and i should ask them how they made it, but what if there is no big need in extended file? Maybe i can use only forward to classify my sample or it will increase the inaccuracy of the classif ...
written 9 months ago by life999450
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what read should i use for classifying?
... Hi, I have forward, reverse and extended illumina myseq 16s rRNA v4-v6 amplicon reads. Length of v4-v6 region is about 520-530 bp while my forward and reverse reads length is only 250 bp each. I checked all three of them in fastqc and it appears that forward read is the best. Should i use forward ...
fastqc forward reverce reads written 9 months ago by life999450

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