I want to map my raw reads (single, 150nt) to my de novo assembled transcriptome (assembled using CLC assembly_cell). Is not a model organism, and I don't have genomic information neither. I made a .gtf file whose first line looks like this (and all the following 750.000 rows follow the same pattern):
contig_1_1 de_novo_assembly exon 1 589 . . . gene_id "contig_1_1"; transcript_id "contig_1_1";
After building the bowtie2 index I run the command line for tophat:
tophat -o /mnt/scrap_disk/zfg1601/TopHat/02 -i 50 -p 6 --library-type fr-unstranded --b2-very-sensitive --no-coverage-search --GTF ZFG-16-01_01_10_Gonad_Filtered_index.gtf ZFG-16-01_01_10_Gonad_Filtered_index filtered_ZFG-16-01_02_17138_TGACCA_L001_R1_001.fastq.gz,filtered_ZFG-16-01_02_17138_TGACCA_L002_R1_001.fastq.gz;
And I get the following error: Error at parsing .tlst line (invalid strand): 0 contig_1_1 contig_1_1. 1-589 (ERR): bowtie2-align exited with value 141.
I then changed the 7th column (strand) and replace the dot with a +, and then it worked. So now I know where the problem is, but still cannot solve it because I don't know the strand of each of my de-novo assembled contigs and apparently I cant run that command without a + or a -. Does somebody know how can I solve this problem? Should I maybe add some extra flag in the command?? Thanks a lot for the help you can provide!