Hi there.
first, I tried to look in those links for my anwser:
but it didn't help.
I have some RNAseq data from Leishmania braziliensis ando also the anotaded genome. The transcriptomes are made of cDNA from mRNA and runned in Illumina. I must retrieve the 3'-UTR from all genes.
First I tried to write a small script calling those sequences by reads mapping, but sometimes the 5'-UTR from the next gene is too close or inside the 3'-UTR, so it's difficult to automate.
Then I tried to assembly the transcriptomes and align the contigs against annotated CDS to retrieve the 3'-UTR. It seems to work, but most times the 3'-UTRs came without polyAs. Is it correct?
Are there some good softwares to retrieve 3'-UTR easily?
thankyou very much.
Rondon
first, I tried to look in those links for my anwser:
but it didn't help.
I have some RNAseq data from Leishmania braziliensis ando also the anotaded genome. The transcriptomes are made of cDNA from mRNA and runned in Illumina. I must retrieve the 3'-UTR from all genes.
First I tried to write a small script calling those sequences by reads mapping, but sometimes the 5'-UTR from the next gene is too close or inside the 3'-UTR, so it's difficult to automate.
Then I tried to assembly the transcriptomes and align the contigs against annotated CDS to retrieve the 3'-UTR. It seems to work, but most times the 3'-UTRs came without polyAs. Is it correct?
Are there some good softwares to retrieve 3'-UTR easily?
thankyou very much.
Rondon
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