Steps taken:
KEY:
MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)
1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam
KEY:
transcripts.gtf (transcripts assembled from step 1)
Homo_sapiens.GRCh37.58.gtf ("reference" annotation from Ensembl)
2. cuffcompare -r Homo_sapiens.GRCh37.58.gtf transcripts.gtf
PROBLEM: The .tmap file lists all assembled transcripts as 'unknown intergenic transcripts' (class code "u")
Would this make sense if there wasn't any MCF-7 transcripts in the supplied reference file? Or how could this be?
Thanks for any help you can offer.
KEY:
MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)
1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam
KEY:
transcripts.gtf (transcripts assembled from step 1)
Homo_sapiens.GRCh37.58.gtf ("reference" annotation from Ensembl)
2. cuffcompare -r Homo_sapiens.GRCh37.58.gtf transcripts.gtf
PROBLEM: The .tmap file lists all assembled transcripts as 'unknown intergenic transcripts' (class code "u")
Would this make sense if there wasn't any MCF-7 transcripts in the supplied reference file? Or how could this be?
Thanks for any help you can offer.
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