Any one work with colorspace data and have experience with Shrimp? I'm starting to work with such data and am exploring my options...
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No, I think Shrimp is just too slow for the number of reads you get. I will try to do a comparison with ZOOM! and BFAST next week though, mainly for aligning reads that were discarded by corona. -
Thanks! This saves me time to figure out Shrimp... I look forward to your comparison between Zoom and Bfast.
I do something similar for Illumina - first Eland and then Bowtie...Comment
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Chipper.. have you tried CLC Bio?Comment
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How about MAQ?Comment
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I hated Corona for my applications. I liked SHRiMP for shorter reads (25 nt) but it's too slow for longer reads. Currently testing ZOOM, which looks good. Interested in other suggestions within reasonable academic means....Comment
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although MAQ is not truly designed to work with SOLiD data, so functions have been added to convert solid reads to fastqComment
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(correct me if I'm wrong)
When colorspace data is converted to sequence, there is a significant loss of information... for example, single mismatch in colorspace may result in 2 mismatches in sequence.
So I think methods that work exclusively in colorspace are preferable.Comment
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Align in colorspace
No doubt about it, alignment needs to be done in colorspace for SOLiD. Makes a significant difference in useable data.Comment
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yeah.. that's interesting cuz I'm sure Heng know about this problem. Perhaps its just a quick hack for now.. and they'll have more in the pipeline.Comment
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