Regarding assemblers
Dear All,
I got a lot of illumina data and AbySS gives me odd errors and fail to complete with test data
For my solexa data it just gives errors taht it cannot read my files.
I have downloaded NCBI SRA_lita data set and to run it too had too convert it to fastq format where a new error is encountered that there are double header information.
I tried every bit to cure it off from fastq-dumpo but its same verytime, though not a n error but for program it wont take it.
and I find few of the sequences have nothing except header information.
Could someone clarify is that happens or I m for a new shock of data missing. Having crosschecked even the RAW data I am dissappointed for getting few no sequence headers.
Is that normal in Illumina.
How to get rid of it. would a perl program help me out ?
m sorry but am too perplexed at present need urgent immediate help.
could someone suggest with confidence built up during their experiments any assemblers I could use with speed and accuracy for my Illumina data set of 48 GB
and if some measure to add up solexa and SOLiD assembly information or read to 454 assembled dataset too !!!!!!!!!!
Thanks in advance.
Regards,
I got a lot of illumina data and AbySS gives me odd errors and fail to complete with test data
For my solexa data it just gives errors taht it cannot read my files.
I have downloaded NCBI SRA_lita data set and to run it too had too convert it to fastq format where a new error is encountered that there are double header information.
I tried every bit to cure it off from fastq-dumpo but its same verytime, though not a n error but for program it wont take it.
and I find few of the sequences have nothing except header information.
Could someone clarify is that happens or I m for a new shock of data missing. Having crosschecked even the RAW data I am dissappointed for getting few no sequence headers.
Is that normal in Illumina.
How to get rid of it. would a perl program help me out ?
m sorry but am too perplexed at present need urgent immediate help.
could someone suggest with confidence built up during their experiments any assemblers I could use with speed and accuracy for my Illumina data set of 48 GB
and if some measure to add up solexa and SOLiD assembly information or read to 454 assembled dataset too !!!!!!!!!!
Thanks in advance.
Regards,