Hello All,
I am having trouble with illumina paired-end 25mer reads and TopHat. The fragment length range was 400-600bp, so there should be mate pairs mapping to different exons. I have used the Galaxy installation of TopHat on the main page. Mate Pair files were generated using the Galaxy grooming and splitting tool. Do each of the read IDs within the split files need a _1 and an _2? The mate pairs are in the same order in each file.
I specified the Mean Inner Distance b/w Mate Pairs as 450 with a Std Dev of 58, Min intron length 70, Max intron length 500000, Min length of read segments 25, NOT using own Junctions.
Output files show 24mil accepted hits, but all show a CIGAR value of 25M, and the splice junction file is empty. Additionally, Cuffcompare to Hg18 Refgene using the Accepted hits file shows no muliti-exon transcripts.
Thanks in advance,
Erick
I am having trouble with illumina paired-end 25mer reads and TopHat. The fragment length range was 400-600bp, so there should be mate pairs mapping to different exons. I have used the Galaxy installation of TopHat on the main page. Mate Pair files were generated using the Galaxy grooming and splitting tool. Do each of the read IDs within the split files need a _1 and an _2? The mate pairs are in the same order in each file.
I specified the Mean Inner Distance b/w Mate Pairs as 450 with a Std Dev of 58, Min intron length 70, Max intron length 500000, Min length of read segments 25, NOT using own Junctions.
Output files show 24mil accepted hits, but all show a CIGAR value of 25M, and the splice junction file is empty. Additionally, Cuffcompare to Hg18 Refgene using the Accepted hits file shows no muliti-exon transcripts.
Thanks in advance,
Erick