search

LangilleLab / microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
GNU General Public License v3.0
437 stars 205 forks source link

About paired-end fastq data #23

Closed cam315 closed 6 years ago

cam315 commented 6 years ago

@mlangill I am new to metaphlan2 and humann2. My question is related to the paired-end data. What will a good solution for paired end data? In addition, shall I directly feed the raw fastq data to metaphlan2.py or it is better to put the fastq file after quality control or assembling? Thank you in advance

gavinmdouglas commented 6 years ago

Hi @cam315, the humann2 authors address this question here: https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-humann2-and-paired-end-sequencing-data

It is definitely better to quality control your reads before running metaphlan2 (you'll be less likely to get false positives).

There are google groups for both the humann2 and metaphlan2 tools, which you may find useful by the way.

cam315 commented 6 years ago

@gavinmdouglas Thank you for your explanation. Sorry to have disturbed you with this question here, I should have checked the user manual carefully.