Hello all,
I have just been trying out the Partek Genomics Suite beta 6.5 release which includes an RNA-seq workflow. I have successfully imported and processed Illumina reads that were already aligned using ELAND (the s_1_sorted.txt file). However, in trying to import raw reads (s_1_sequence.txt) in fastq format and performing the alignment from within Partek using bowtie, I run into problems. The import appears to work fine, and I then see a summary of the number of aligned reads per file/lane. But when I try to then map the reads to RefSeq or AceView genes, I get all zeros in the raw and RPKM read counts columns.
Is anyone else using the Partek RNA-seq workflow with Illumina fastq output? Any ideas where the issue might lie?
Thanks,
Matt
I have just been trying out the Partek Genomics Suite beta 6.5 release which includes an RNA-seq workflow. I have successfully imported and processed Illumina reads that were already aligned using ELAND (the s_1_sorted.txt file). However, in trying to import raw reads (s_1_sequence.txt) in fastq format and performing the alignment from within Partek using bowtie, I run into problems. The import appears to work fine, and I then see a summary of the number of aligned reads per file/lane. But when I try to then map the reads to RefSeq or AceView genes, I get all zeros in the raw and RPKM read counts columns.
Is anyone else using the Partek RNA-seq workflow with Illumina fastq output? Any ideas where the issue might lie?
Thanks,
Matt
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