Hi fabrice,
Here are a few things for you to consider when trouble shooting:
1) use fastqc to check the quality of your reads
2) use fastx toolkit to check the length distribution of your trimmed reads. One thing to find out is whether most of the trimming is from 3'-end. If it is, you may trim the reads by fixed number of nts so you have uniform read length.
3) BWA alignment results are useful but I would use Bowtie to align the reads and check the mapping statistics, as Tophat uses Bowtie to map so the results are more relevant
4) Start with Tophat default and mandatory parameters to see if you can get decent results
Hope this helps.
Douglas
Here are a few things for you to consider when trouble shooting:
1) use fastqc to check the quality of your reads
2) use fastx toolkit to check the length distribution of your trimmed reads. One thing to find out is whether most of the trimming is from 3'-end. If it is, you may trim the reads by fixed number of nts so you have uniform read length.
3) BWA alignment results are useful but I would use Bowtie to align the reads and check the mapping statistics, as Tophat uses Bowtie to map so the results are more relevant
4) Start with Tophat default and mandatory parameters to see if you can get decent results
Hope this helps.
Douglas
Comment