Hi All,
My RNA-seq data has low qualities in the tail. So I trimmed the reads which leads to my reads with variable length. TopHat support variable read analysis.
But when I fed them to Cufflinks which will estimate the fragment length distribution estimation, I wonder how cufflinks address the variable length to get the fragment length.
And I checked the alignment of TopHat.
100872499 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
100872499 + 0 mapped (100.00%:nan%)
100872499 + 0 paired in sequencing
43961266 + 0 read1
56911233 + 0 read2
2486806 + 0 properly paired (2.47%:nan%)
59365252 + 0 with itself and mate mapped
41507247 + 0 singletons (41.15%:nan%)
You can see that the number of properly paired reads are small. Does Cufflinks estimate the read length based on the properly paired reads or re-estimate all the mate mapped reads.
Many thanks for your help.
My RNA-seq data has low qualities in the tail. So I trimmed the reads which leads to my reads with variable length. TopHat support variable read analysis.
But when I fed them to Cufflinks which will estimate the fragment length distribution estimation, I wonder how cufflinks address the variable length to get the fragment length.
And I checked the alignment of TopHat.
100872499 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
100872499 + 0 mapped (100.00%:nan%)
100872499 + 0 paired in sequencing
43961266 + 0 read1
56911233 + 0 read2
2486806 + 0 properly paired (2.47%:nan%)
59365252 + 0 with itself and mate mapped
41507247 + 0 singletons (41.15%:nan%)
You can see that the number of properly paired reads are small. Does Cufflinks estimate the read length based on the properly paired reads or re-estimate all the mate mapped reads.
Many thanks for your help.
