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Question about RiboTools Kmer analysis - phasing
24-Apr-2017, 05:42 PM
Post: #3
RE: Question about RiboTools Kmer analysis - phasing
(24-Apr-2017 02:27 PM)jamesp Wrote:  Hello,
we think this issue is because you used a fasta file (from UCSC) and a GFF3 file (from Ensembl) from different sources.
We suggest you also use the corresponding fasta file for your dataset from Ensembl. It looks like kmer while its able to count the number of reads cannot match the gene names to the GFF3 file.
Unfortunately this is a bit of rework to obtain the sorted bam file.
Thanks to let us know if this works.

Kind Regards
jamesp

Thank you, James. I redid the alignment with the fasta file I obtained form Ensemble. Now when I do the Kmer analysis, I receive an error like the one below.

Quote:Error during footprinting : list index out of range
Programme aborted at Mon Apr 24 18:35:14 2017

Begin kmer and phasing analysis at Mon Apr 24 18:34:55 2017
2295780 reads are presents in your bam file


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RE: Question about RiboTools Kmer analysis - phasing - jjb91 - 24-Apr-2017 05:42 PM

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