changing Mito to Mt and vise versa is too confusing

Question

[zizigolu]

Hi,

I am using Scharomyces Bowtie2Index and genome.fa, gtf from ensembl for tophat2, cufflinks and cuffmerge...but always changing between two errors, once could not find Mito in fasta once could not find Mt...and an infinite cycle while I am changing Mito to Mt or vise versa and realigning for many hours...may you please tell me a solution to get rid of this confusing problem?

Thank you

Answer 1

[Sean Davis]

You could simply change everything to either Mt or Mito before starting or, perhaps better, get all your information from one source (eg., get genome and gtf from ensembl). I have found, though, that it is definitely best to do this before starting with any analysis.

[zizigolu]

thank you, i am using genome.fa, gtf and all from ensembl sourse but as i read in biostar its not enough to change because im using pre-build bowtie2-index from ensembl and might the genome.fa with Mito already indexed while i am changing that to Mt to use in cuffmerge...in other hand i dont know how to build genome index when using tophat2..really confusing

[zizigolu]

sorry I changed Mt to Mito but in gtf and genome.fa but again this error

[Sean Davis]

You'll have to rebuild your bowtie index after you make any changes to the fasta file.

[zizigolu]

thank you, i saw i should find another source in which i don't have to change genome.fa instead it's ok changing gtf