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ndaniel / fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data
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Meaning of tags 't3, t4, t7' etc in fusion description column #200

Open asmitagpta opened 2 years ago

asmitagpta commented 2 years ago

Hi,

I am running fusioncatcher v1.33 for a set of RNA-Seq data. I noticed that the output file for many of the samples contain fusions with t3, t4, t7 tags in their fusion description column, but I can't find their corresponding meaning in the manual on github.

FTX pseudogene,lncrna,**t3** 11.0 3.0 20.0 39.0 BOWTIE+STAR 2:222699022:- X:74278373:- ENSG00000203531 ENSG00000230590 AGATCGTGCCACTGCACTCCAGCCTGGCGACAGAGTGACACTCCGTCTCA*AAAAAAAAAAAGAAACGATCACATCCAGATGTCCTGTTACTGGAAGGGCA exonic(no-known-CDS)/exonic(no-known-CDS) AD1889_2T left_only

VPS4B **t3** 0.0 3.0 3.0 39.0 BOWTIE+BLAT;BOWTIE+STAR 9:68250495:- 18:63396911:- ENSG00000279706 ENSG00000119541 TGGAGTGCAGTGGCGTGATCTCGGCTCACCATAACCTCCGCCTCCCAGCT*TTCAAGCAATTCTCATGCCTTAGCCTCCTGAGTAGCTGGAATTACAGGCG exonic(no-known-CDS)/UTR AD1889_2T left_only

GON4L lncrna,**t3**,100K<gap<200K 0.0 3.0 2.0 41.0 BOWTIE+BLAT;BOWTIE+BOWTIE2;BOWTIE+STAR 1:155763312:- 1:155637492:- ENSG00000116580 ENSG00000287839 TGCTTCACCTGAGACTGCTCCAGAAGTGGAGACCAGCAGAACTCCACCAG*CCTGTGAAACCACGAACCCTTCAATCAAGAAAAGACCTTTGATCAGGAGA CDS(truncated)/exonic(no-known-CDS) AD1889_2T left_only

ATP1B1 USP7 cancer,**t4**,short_repeats,sr1.09 0.0 4.0 15.0 21.0 BOWTIE+STAR 1:169132029:+ 16:8966733:- ENSG00000143153 ENSG00000187555 AAGGTGTAAATATTCAACGGGAATAAAACTGGCATGGTAATTTTTTTTTT*TTGTGTGTTTTTTGTTTTTTGTTTTTTGTTTTTTTTTGACACAGAGTCTC UTR/intronic AD1890_3T left_only

SPTAN1 GPCPD1 cancer,m6,**t7** 0.0 7.0 2.0 34.0 BOWTIE+BOWTIE2 9:128599412:+ 20:5598821:- ENSG00000197694 ENSG00000125772 AACCTCAGGTGATCTGCCCACCTCAGCTTCCCAGAGTGCTGGGATTACAG*GAGAAGTTTTTGCGATATGTGGAAGCTGTGATGCTTTGGGAAACTGGAAT UTR/CDS(truncated) AD1892_5T left_only

What do these tags mean?

xiucz commented 2 years ago

@ndaniel Can you take a look at this question? I am also curious about it. Thank you! Best, xiucz

ashleethomson commented 1 year ago

Commenting to keep this open, because I have the same question and still can't find anything to explain it. I have everything from t1 to t17. I've noticed that the same fusion (if it appears multiple times) has the same t#.