I am working on the zebrafish genome. I took out two regions of the genome hence called good and tricky
good: chr1 44689765 44728408
tricky: chr1 44619749 44656560
From my BAM file, reads mapped on the ZV9 (danRer7) genome I extracted subset BAM files for these two regions. Cufflinks is able to assemble transcript from the good region, while giving nothing in the tricky region.
Both the regions have decent coverage and reads map in agreement with ensembl gene models (v71). The tricky region has many reads with "Alignment not primary" status. The mapped BAM files can be easily visualised in the IGV browser, selecting the zebrafish genome (Zv9).
URL access: http://dl.dropboxusercontent.com/u/18397852/bam.zip
This behavior of Cufflinks completely confused me and I am wondering if there is a problem in its approach to assembly.
good: chr1 44689765 44728408
tricky: chr1 44619749 44656560
From my BAM file, reads mapped on the ZV9 (danRer7) genome I extracted subset BAM files for these two regions. Cufflinks is able to assemble transcript from the good region, while giving nothing in the tricky region.
Both the regions have decent coverage and reads map in agreement with ensembl gene models (v71). The tricky region has many reads with "Alignment not primary" status. The mapped BAM files can be easily visualised in the IGV browser, selecting the zebrafish genome (Zv9).
URL access: http://dl.dropboxusercontent.com/u/18397852/bam.zip
This behavior of Cufflinks completely confused me and I am wondering if there is a problem in its approach to assembly.
