Hi,
I'm working with Illumina GAII data (5 million reads) from a 5' cap capture library. I did the mapping against a transcriptome with ELAND_standalone and now I'm left with 500000 reads that were mapped to a Gene-ID (after filtering). Most of the reads had more than one hit or had one or two mismatches. I used the default values for the filtering (not sure if I can change these with the standalone).
Now I just want to know if you get the same numbers (only 10 % mappable reads) with your data or if that number is too low.
I'm working with Illumina GAII data (5 million reads) from a 5' cap capture library. I did the mapping against a transcriptome with ELAND_standalone and now I'm left with 500000 reads that were mapped to a Gene-ID (after filtering). Most of the reads had more than one hit or had one or two mismatches. I used the default values for the filtering (not sure if I can change these with the standalone).
Now I just want to know if you get the same numbers (only 10 % mappable reads) with your data or if that number is too low.
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