Entering edit mode
7.8 years ago
jz6002
▴
10
I have download the Genesplicer and ran it as
/bin/linux/genesplicer fastq-file human -f output_file_name
Then, I got no error message in the console and my output file is empty. Does anyone know if the software has a specific length for the input sequence or did I do something wrong?
I have tried to contact the author of the software, but no one replies. So I tried my luck here.
Thank you.
Maybe try running the tool with a representative subset of the input file if the input file is too large?
The input file has only one sequence.
http://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml
According to this site, the input should be (may be?) the following:
" Input sequences may be in FASTA format or simple DNA sequences".
I am not sure fastq-format existed at the time the program was created.
https://en.wikipedia.org/wiki/FASTQ_format
I tried input file as "simple DNA sequences", I got error message as "The input file is not a fasta file" Then I tried a input file such as
I got no error message, but also no output. If it does need a fasta file, how can I get that from a vcf file? All I have is a list of variants or a vcf file. I can use bedtools to get the sequences based on the position of the variants. It seems impossible for me to get a fasta file from the data I have....
But you still have your RNA as a fastq-file with several variants, am I correct?
Let's start from the very beginning. You have some human RNA sequence as a fastQ-file, this is all I know.
You were going to use Genesplicer. Try to find another program with a desired output.
There was a post: FASTQs to the VCF It may help you.
This post below suggested some possibility to go from fastq to fasta with Galaxy and also without Galaxy (in the end).
You will get fasta-variants consensus. How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
Actually, I am asking to make a pipeline which takes in mRNA id such as: NM_058216.2:c.571+4A>G Then, output all the annotations I can get for it. The result of GeneSplicer is one of the annotations.
I believe GeneSplicer should be able to work with just sequence data. Because for software like alamut, it can provide GeneSplicer result just based on the above mRNA id.