Tophat2 command analysing

Question

[worarado.kan]

I try running mapping to reference using tophat -cluffink after I run bowtie2-build I get GDDH13_1-1_formatted.1.bt2 GDDH13_1-1_formatted.2.bt2 GDDH13_1-1_formatted.3.bt2 GDDH13_1-1_formatted.4.bt2 GDDH13_1-1_formatted.rev.1.bt2 GDDH13_1-1_formatted.rev.2.bt2

Next I have to run tophat2 but I have a problem, so what is the command i should use for running tophat2?

Please recommend me.

[bioinfo_ga]

tophat-2.0.13.Linux_x86_64/tophat -G ref.gtf --output-dir out index_prefix input_reads.[fasta|fastq]] Try using this command

[worarado.kan]

Thank you for your message

[worarado.kan]

Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (GDDH13_1-1_formatted.2.bt2.*.bt2l) [hscience@localhost Tophat2]$

it always showed error. I dont understand why can not find index

[Fatima]

Are you running from the Tophot2 folder? It's better to run from the folder that contains the data so you don't need to add the path to the directory. Also you can use ll or ls -l in your folder to make sure the files are readable.

http://linuxcommand.org/lc3_lts0090.php

[Fatima]

These links might help:

http://www.sthda.com/english/wiki/tophat2-download-build-reference-genome-and-align-the-reads-to-the-reference-genome

https://github.com/Jeanielmj/bioinformatics-workshop/wiki/Read-Alignment-with-TopHat2

TopHat2 command usage:

tophat2 [options]* <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]

Input:

genome_index_base : the basename of the genome index to be searched
reads1_1[,...,readsN_1] : a comma-separated list of files containing reads in FASTQ format. When running TopHat with paired-end reads, this should be the *_1 ("left") set of files.
[reads1_2,...readsN_2] : A comma-separated list of files containing reads in FASTQ or FASTA format. Only used when running TopHat with paired end reads, and contains the "_2" ("right") set of files. The "_2" files MUST appear in the same order as the *_1 files.

[worarado.kan]

Thank you so much for information