Extracting sequences from bed file using tools extract Genomic DNA tool and bed to Fasta tool

[Akash_Ajay]

Hello everyone,

I have set of genomic intervals of yeast that I was able to write in BED Format. I gave the build s288c S cerevisae for the bed. In tools of both getFastabed and extract genomic DNA ,I gave this bed file as input and for reference genome I gave the FASTA file of s288c S.cerevisae, which I downloaded from NCBI site.
The job is getting executed, but I am getting a file with 0 bytes. I have seen similiar problem in the community and tried to follow those steps, but no avail. I even tried trial and error to solve the problem but no avail.
I have referred to this thread to troubleshoot-Extract Genomic DNA won't work
I am attaching screenshots for your kind reference- ( a sample BED file and error)

I am not able to figure out where I am going wrong. Please help
Thank you

[Akash_Ajay]

resolved , thank you

[jennaj]

Hi @Akash_Ajay

Glad you solved the problems. It appears that the mismatched chromosome names were at least part of the original problem (based on your screenshots).

For others reading, more about properly formatted and content matched inputs:

• Content:
  • Preparing and using a Custom Reference Genome or Build
  • Mismatched Chromosome identifiers (and how to avoid them)
• Format:
  • Format help for Tabular/BED/Interval Datasets
  • Common datatypes explained – see fasta, bed, interval

[Akash_Ajay]

Thank you madám, the links are very helpful. Thanks again