I'm using ABySS to assemble Illumina ChipSeq data. The data is a fastq file. I would like to know whether quality scores/quality trimming is processed during ABySS assembly. Or I have to do quality trimming the fastq file before running ABySS. Thanks!
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Why do you want to assemble ChIP-seq data? The usual workflow is to map the sequences to a reference genome and then use a peak calling program to identify enriched regions. -
The genome we're interested is not available yet. Thus, we are trying to assemble contigs.Comment
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Hi,
I clean my reads using home brewed scripts. I FASTQ->FASTA, then submit the fastA reads to ABySS. This reads can also be used to feed other tools like velveth. Sorry if this respond is late.
HTH
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