Ferreira GC, Oberstaller J, Fonseca R et al. Iron Hack; F1000Research 2019, 8:1135 [version 1; peer review: 2 approved] doi:10.12688/f1000research.19140.1
MassiveSeq’s implementation of HISAT2 and StringTie identified novel-isoform transcripts in various samples. We focused our analyses on the FXN gene, as trinucleotide GAA-repeats at this locus are causative of FRDA. We identified multiple novel-isoform transcripts within 1kb up and downstream of FXN in affected, unaffected and carrier-patients (Table 2). We were able to visualize the truncation of the FXN transcripts from the above samples using IGV. Shallow read-coverage of the whole transcriptome from this particular study made it difficult to confirm the reliability of the identified transcript truncation.
Common questions in the community about hackathons include whether they can focus on specific diseases and how clinical personnel can interact more effectively with data scientists. We found that it was indeed possible to focus on a given disease while developing generalized tools in a hackathon. In fact, we found it helpful to have cases to use in our analyses from a specific disease. Finally, we found it was to the benefit of everyone to have clinical personnel involved, especially in the later stages of the event.
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