how to convert mirna hsa.gff3 to hsa.gtf?

Hi,

is there any script that I can use to convert hsa.gff3 to hsa.gtf? I am newbie on using STAR and RNA-seq. apparently to get read counts I need to feed it into STAR

thanks Sara

rna-seq

• 1,830 views • link

updated 9.3 years ago by Biostar

• written 9.4 years ago by jonessara770

Three posts with suggestions here, here and here.

• 0 views • link

written 9.3 years ago by h.mon

0 answers

No answers yet.

More posts like this

How can I download the fasta file of RepeatMasker UCSC table directly?
written 8.0 years ago by jonessara770

Hi, I am a newbie in Retrotransposable/repeat elements analysis. I used UCSC table in order to get the sequence of RepeatMasker table in fasta format. …
duplicate read names in TCGA raw bam file
written 9.2 years ago by jonessara770

Hi, I downloaded some TCGA ExomeSeq bam file and would like to convert them to fatsq. Picard can not convert them because there are some …
why remove adapter just from 3' of the reads
written 9.4 years ago by jonessara770

Hello, I wonder why we just remove adapter from 3' end of reads and not both sides? For example when using Illumina TruSeq™ Small RNA, …
best STAR options for miRNA mapping?
written 9.4 years ago by jonessara770

Hello, I am a newbie in STAR. my questions: Do you use STAR for mapping miRNA? can you share the command lines that you use …
how to extract human from mature.fa?
written 9.4 years ago by jonessara770

Hello, I downloaded mature.fa files from mirbase database. it contains all of species but i want only human. is there any script/ Rpackage ect to …
calculate haloplex coverage
written 9.4 years ago by jonessara770

Hi, How do you calculate the coverage of target genes with Haloplex data? I am trying to use GATK but it gives 0 for TP53. …
Threshold for variant detection by Haloplex
written 9.4 years ago by jonessara770

Hi guys, I am newbie in Haloplex data analysis. I have haloplex data from few tumor and normal samples. I mapped them by BWA and …
what chipseq marker(s) we should use to study the effect of HDAC?
written 9.6 years ago by jonessara770

Hello, I am a newbie in epigenome. I wonder what histone marks I should use if I want to study the effect of HDAC in …
run our pipeline on TCGA data
written 9.6 years ago by jonessara770

Hello all, I am wondering if it is possible to run our own pipeline (WES, WGS or RNA-Seq) on TCGA raw data without downloading TB …
How to get counts of STAR output (sam/bam).
written 10.2 years ago by Shahzad •

Dear Members I am working on RNA-seq differential expression. I have aligned my RNA reads on reference genome using STAR. I need to know to …