Error: gtf_to_fasta returned an erro - Is there any better Rice gtf file for RNAseq is available?
Recently I updated tophat pipeline to tophat2 and and bowtie2. I was trying to working on DEGs in Oryza sativa (japonica species) using Illumina paired end reads and got the error Error: gtf_to_fasta returned an error.
tophat2 --GTF all.gff3.txt -o result2 riceindex 5D-con1_1_val_1.fq 5D-con1_2_val_2.fq
From previous posts, I came to know that
- inconsistencies in chr naming between GTF file and index file is one possible reason. But my gff3 file from RGAP worked well with tophat older version. (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.gff3).
Another possibility suggested was orphan reads after adapter removal. But I used Trim galore+ cutadap wrapper tool for this purpose, as below
trim_galore -paired -phred333 -q 20 -a adapterseqence -stringency 5 -e 0.1 -t -r1 35 -r2 35 set1_1.fq set2_2.fqAnother post suggested the non-compatible index and annotation file can also make problem. I used IRGSP 5 for building index file. Can anyone please tell me what is the wrong things am doing? Also is there any other better file source for Rice RNASeq analysis?
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If you are able to use the sequence/annotation/aligner index bundle for Rice found on iGenomes site you may be able to avoid this sort of issues: http://support.illumina.com/sequencing/sequencing_software/igenome.html
Thanks for reply @genomax2. I checked the link which you provided. But the files looks the older one. As I know MSU has version 7 now and IRGSP build 5 is available . Do you have any comments?
Do either of those locations make a package (sequence/annotations) available? If they do I would say choose that and then build your own aligner indexes for bowtie2.
Thanks @genomax2. I will make a try..!!