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nghiavtr / FuSeq

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Gene symbol missing in calls, no placeholder present #17

Open mapostolides opened 3 years ago

mapostolides commented 3 years ago

Hello,

Just wanted to point out a bioinformatic challenge with downstream data processing. Your tool seems to leave the "symbol5" or "symbol3" field blank on occasion:

gene5   chrom5  strand5 brpos5  cds.brpos5.start        gene3   chrom3  strand3 brpos3  cds.brpos3.start        fusionName      symbol5 symbol3 SR.passed       MR.passed       supportRead     score   info
ENSG00000257207 2       -       111181238       111181298       ENSG00000144063 2       -       110849347       110849347       ENSG00000257207-ENSG00000144063         MALL    0       14      16      16

In this case, the head gene name "AC112229.3" is not provided, which leaves the line with 16 columns instead of 17. This can break bioinformatics workflows downstream. Some sort of placeholder would prevent this (e.g. ".", or "N/A" ).

nghiavtr commented 3 years ago

Dear @mapostolides,

Many thanks for your suggestion to improve FuSeq. This issue has been fixed in the new version of FuSeq (v1.1.4).

Best, Nghia