Question: Find exogenous sequences like EGFP in RNA-seq data
gravatar for whiter
4.0 years ago by
whiter0 wrote:


I am mapping some data from EGFP+ and EGFP- samples. I want to confirm that they are what I think they are by making sure they do or do not have GFP reads.

I tried making a custom genome containing only EGFP and mapping against that using "custom builds" but got the error below. But this might not even be the best way, so any ideas are appreciated.


Traceback (most recent call last):
  File "/galaxy-repl/main/server/lib/galaxy/datatypes/converters/", line 52, in <module>
    compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True )
  File "/galaxy-repl/main/server/lib/galaxy/datatypes/converters/", line 47, in compute_fasta_length
    fasta_title = fasta_title.split()[0]
IndexError: list index out of range



rna-seq egfp • 1.5k views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by whiter0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This appears to be due to format problem in the custom genome fasta dataset. Perhaps the lines are not wrapped? Help to solve this and other format problems are in the links below:

Best, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
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