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compmetagen / micca

micca - MICrobial Community Analysis
http://compmetagen.github.io/micca
GNU General Public License v3.0
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question about Mergepairs command #11

Closed Alfredssss closed 7 years ago

Alfredssss commented 7 years ago

Hi, When I use

micca mergepairs -i _R1.fastq -o Merged.fastq

it automatically recognize the R2 file? or I have to repeat the same command with R2 and then merge the two file sets? thank you for the attention

davidealbanese commented 7 years ago

Dear @Alfredssss, in this case the command recognizes automatically theR2 file but probably you mean:

micca mergepairs -i *_R1.fastq -o Merged.fastq

When only the option -i is specified (and not the option -r/--reverse) the reverse file name will be automatically constructed by replacing the string _R1 in the forward file name with the corresponding _R2 (default behaviour see options -p/--pattern and -e/--repl). You can also customize the replacing options, e.g. the command:

micca mergepairs -i *READ1.fastq -o merged.fastq -p READ1 -e READ2

will replace READ1 with READ2 searching in every file *READ1.fastq.

Moreover, after the merging of the paired reads, different samples will be merged in a single file and sample names will be appended to the sequence identifier (e.g. >SEQID;sample=SAMPLENAME), as inmicca merge and micca split. Sample names are defined as the leftmost part of the file name splitted by the first occurence of _ (-s/--sep option).

AndreaQ7 commented 7 years ago

Thank you a lot for your explaination!!!