yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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which part should I modify? #141

Open weifei888 opened 3 years ago

weifei888 commented 3 years ago

Firstly, My Bam file was sorted and indexed, the command "samtools view C0_3.sort.bam A01:16818-19507 " showed that there were a lot of reads.

Secondly,I modified the gff file, shown as:

A01 EVM gene 1913 2559 . - . ID=GH_A01G0001; A01 EVM mRNA 1913 2559 . - . ID=GH_A01G0001;Parent=GH_A01G0001; A01 EVM exon 2491 2559 . - . ID=exon:GH_A01G0001:1;Parent=GH_A01G0001; A01 EVM CDS 2491 2559 . - 0 ID=CDS:GH_A01G0001:1;Parent=GH_A01G0001; A01 EVM exon 2255 2365 . - . ID=exon:GH_A01G0001:2;Parent=GH_A01G0001; A01 EVM CDS 2255 2365 . - 0 ID=CDS:GH_A01G0001:2;Parent=GH_A01G0001; A01 EVM exon 1913 2134 . - . ID=exon:GH_A01G0001:3;Parent=GH_A01G0001; A01 EVM CDS 1913 2134 . - 0 ID=CDS:GH_A01G0001:3;Parent=GH_A01G0001;

The gff was indexed by code "index_gff --index tm-1.gff tm-1"

And I ran: miso --run tm-1 C0_3.sort.bam --output-dir C0_3 --read-len 150 --paired-end 250 15 --settings-filename miso_settings.txt

Then many directions were generated, however there was no result in each chromosome direction

I checked the log in batch-logs, there were some read, shown as:

Only 5 reads in gene, skipping (needed >= 20 reads) Computing Psi for 1 genes...

So I am wondering if it is possible that you can show me which part should I to modify?