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OpenGene / AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
MIT License
206 stars 51 forks source link

Plans for reading .gz ? #6

Closed colindaven closed 8 years ago

colindaven commented 8 years ago

Hi, nice tool.

Are there any plans for reading gzipped files in the future ? This can be quite helpful, especially when reanalyzing quality of older compressed projects.

Also, is there an internal adapter library or does AfterQC find adapters by itself in the reads ? I couldn't understand the command line help about barcodes.

Thanks. Colin

sfchen commented 8 years ago

gz is already supported, if you have any problem using it to parse gz file, update here.

AfterQC currently does adapter trimming automatically if it meets: 1, it is pair-end sequencing 2, the original DNA template is shorter than sequencing cycles, so that it may sequence the adapters in the read1/read2 tail.

Note that Illumina bcl2fastq already supports some adapter trimming now, so you don't need to worry about adapter any more, except the case above.

The barcode in the command line help is only for single molecule barcoding, so just ignore that.

colindaven commented 8 years ago

Ok, thanks! Seems to work well.