hi i would be happy to get some help i wanted to use this web to see the strength of a splice site this is what they are asking How to use MaxEntScan::score5ss Each sequence must be 9 bases long. [3 bases in exon][6 bases in intron] Input sequences as a FastA file with one sequence per line (no linebreaks). Non-ACGT sequences will not be processed.
Example Fasta File
dummy1 cagGTAAGT dummy2 gagGTAAGT dummy3 taaATAAGT
I'm having trouble choosing which column from the rmats output o I need to choose as the pose i will take the sequences (for each type of events i want to take this from this files A3SS.MATS.JCEC.txt A5SS.MATS.JCEC.txt RI.MATS.JCEC.txt SE.MATS.JCEC.txt MXE.MATS.JCEC.txt but im having troubl of choosing the right colunms for ech event type also I wanted to ask for negative stran should I extract the same sequence but us use the complement letters? can someone guide me with this? thanks alote
I will add here the heads of the files so you could see the colunms names
02:~/adi8897/master_project/NOVA2/24_2/rmats% head RI.MATS.JCEC.txt ID GeneID geneSymbol chr strand riExonStart_0base riExonEnd upstreamES upstreamEE downstreamESdownstreamEE ID IJC_SAMPLE_1 SJC_SAMPLE_1 IJC_SAMPLE_2 SJC_SAMPLE_2 IncFormLen SkipFormLen PValue FDRIncLevel1 IncLevel2 IncLevelDifference
<46|0>adi8897@moriah-gw-02:~/adi8897/master_project/NOVA2/24_2/rmats% head SE.MATS.JCEC.txt ID GeneID geneSymbol chr strand exonStart_0base exonEnd upstreamES upstreamEE downstreamES downstreamEEID IJC_SAMPLE_1 SJC_SAMPLE_1 IJC_SAMPLE_2 SJC_SAMPLE_2 IncFormLen SkipFormLen PValue FDR IncLevel1 IncLevel2 IncLevelDifference
<47|0>adi8897@moriah-gw-02:~/adi8897/master_project/NOVA2/24_2/rmats% head MXE.MATS.JCEC.txt ID GeneID geneSymbol chr strand 1stExonStart_0base 1stExonEnd 2ndExonStart_0base 2ndExonEnd upstreamES upstreamEE downstreamES downstreamEE ID IJC_SAMPLE_1 SJC_SAMPLE_1 IJC_SAMPLE_2 SJC_SAMPLE_2 IncFormLen SkipFormLen PValue FDR IncLevel1 IncLevel2 IncLevelDifference
<48|0>adi8897@moriah-gw-02:~/adi8897/master_project/NOVA2/24_2/rmats% head A3SS.MATS.JCEC.txt ID GeneID geneSymbol chr strand longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE ID IJC_SAMPLE_1 SJC_SAMPLE_1 IJC_SAMPLE_2 SJC_SAMPLE_2 IncFormLen SkipFormLen PValue FDR IncLevel1 IncLevel2 IncLevelDifference
<49|0>adi8897@moriah-gw-02:~/adi8897/master_project/NOVA2/24_2/rmats% head A5SS.MATS.JCEC.txt ID GeneID geneSymbol chr strand longExonStart_0base longExonEnd shortES shortEE flankingES flankingEE ID IJC_SAMPLE_1 SJC_SAMPLE_1 IJC_SAMPLE_2 SJC_SAMPLE_2 IncFormLen SkipFormLen PValue FDR IncLevel1 IncLevel2 IncLevelDifference
