Entering edit mode
6.9 years ago
alirezamomeni707
•
0
I have ribosome sequencing data and want to align it to the tRNA (not mRNA transcriptome). I have filtered out rRNA, non-coding RNAs and adapter. also I made tRNA indexes using bowtie2 (I have .bt2 files). now I want to align my data to the tRNA transcriptome. I have tried this command but did not give me BAM file. do you know how to solve the problem.
tophat -n 2 -m 1 --segment-length 25 --no-novel-juncs
--no-novel-indels --no-coverage-search -G gencode.v19.tRNAs.gtf -p 1 -o Ctrl_tophat_out tRNAs Ctrl.fastq.gz
why tophat? you can use bowtie2 for that.
I actually tried did not work. maybe my command was wrong. do you have an example?
You need;
That`s it
what tool do you suggest? actually I need to get bam file.
If for some reason you actually need a splice-aware aligner (unlikely) then you can just use bowtie2 directly.
here is the error I got after running this command:
Edit to show the command you used.