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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
MbandiComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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