Dear all,
I have a simple question: Is it possible to get the genome sequences based on the six bt2 index files created by bowtie2? How to achieve this?
Actually I am writing a simple bash pipeline to conduct RNAseq analysis. TOPHAT2 requires genome INDEX, but does not need genome.fa as input. In contrast, CUFFDIFF has a parameter (-b) for genome.fa, without requiring genome INDEX. So I just want INDEX as input. Thank you very much!
Hello,
In order to get the sequences from which the bt2 index files came from you can use bowtie2-inspect as follows:
bowtie2-inspect <bt2_base>
If you run the command above with your bt2 index files, the tool will output a FASTA file containing the sequences of the original references.
There are also some options available, you can check the bowtie2 manual.
Cheers!
I never knew about this. Thanks for pointing it out. Do you know if there's something similar for bwa?
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