Question: de novo aseembly counting
gravatar for s.good
2.4 years ago by
s.good0 wrote:



I have assembled de novo reference gene and mapped it to tophat now i want to calculate the read count for mapped reads.

For this, i sorted my bam files and used htseq count for counting the reads . I used the gtf file for this.

Ques 1. Htseq is giving 0 for every read count? Why ? But i can see a lot of reads in IGB. Please suggest a way to count the number of mapped reads


Ques 2. When i performed cufflinks with the same gtf file it gave a lot ensemble ids and FPKM but why is HTSeq not working in this case, it is identifying the ensemble ids but giving 0 for every ensemble ids.



What kind  of programs can be used for this?





counting de novo • 679 views
ADD COMMENTlink modified 2.4 years ago by Jennifer Hillman Jackson24k • written 2.4 years ago by s.good0
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson24k wrote:


These problems are often associated with a reference genome mis-match problem between the inputs. In this case, the GTF annotation dataset and the fasta genome used for mapping (either built-in or custom). 

Start by double checking the chromosome identifiers in all inputs. Here is how: Support#Reference_genomes.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson24k

Also see:

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson24k
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