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Extract V3-V4 region for 16S

Dear all, I would like to extract all the v3-v4 region from silva.bacteria.fastq file. After consulting to the MISEQ SOP for mothur, I have used the command line as below. But I'm not sure about the start and end position for V3-V4 region. Would 6388 and 25319 used be the right position? Can someone help to share their experience? Great appreciate for your help.

mothur "#pcr.seqs(fasta=silva.bacteria.fasta, start=6388, end=25319, keepdots=F,processors=8)"

Lola

rna-seq sequence
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updated by Biostar Biostar • written by liqing1123 • liqing1123

2 answers

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written by lakhujanivijay lakhujanivijay

Dear Vijay Thank you for your kind help. I will try this software. Actually mothur can also perform the extraction by the command "pcr.seqs", I just doubt about the start and the end point of V3-V4 in SILVA Bacteria fasta file and highly apprecate if someone can share the number with me. Thank you again for your fast and helpful answer.

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written by liqing1123 • liqing1123

I wonder what shall be the objective to extract the V3-V4 regions? Wouldn't your data had already captured those regions. I believe if you are performing the taxonomic abundance study, you can easily use QIIME

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written by lakhujanivijay lakhujanivijay

See this blog post and the last comment on that page: http://blog.mothur.org/2016/07/07/Customization-for-your-region/

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written by Fedor Gusev Fedor Gusev

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