Question: Map reads to cDNA gtf file
gravatar for elena
4.1 years ago by
elena0 wrote:


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!

rna-seq assembly • 1.0k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by elena0
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

You can directly use bowtie2 for aligning again an assembled transcriptome.

ADD COMMENTlink written 4.1 years ago by Devon Ryan96k
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