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Old 11-20-2015, 02:12 PM   #1
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Question TopHat2 command

Hello, I am not a bioinformatician I am more of a bench scientist. I am trying to align illumina bodymap 2.0 RNAseq files from ENA to the hg19 .fa file. I cannot find the command anywhere to do this with tophat. Is it similar to the bowtie2 command? I just started using linux to get this data and I really need help .
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Old 11-20-2015, 02:51 PM   #2
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First, you want to be sure you have a powerful enough computer, and enough disk space.

Second, you want to build an index for the hg19.fa file or download one, from the iGenomes for example

Third, you'll want to download the annotation file, in the format of a GTF file, from UCSC or the iGenomes.

Fourth, you need to understand the Linux command line.
To get the arguments for TopHat, just run the following command.

tophat --help
Here is a sample command for TopHat
tophat \
--library-type fr-firststrand \
-G Mus_musculus.GRCm38.77.gtf \
-o results/tophat/sample_1 \
Bowtie2Index/Mus_musculus.GRCm38.dna.primary_assembly \
sample_1_R1.fastq.gz \
There is a classic article in Nature Protocols for beginners.
They make it sound a bit too simple, though, and don't cover any of the subtleties of RNA-Seq.
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Last edited by blancha; 11-21-2015 at 02:22 PM.
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Old 11-21-2015, 04:57 AM   #3
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@fk566938: If you want to avoid the time consuming step of aligning the files (sounds like you are a new user and may not have adequate software/hardware available locally) you could use the aligned BAM files that were made available by Ensembl for this data.

Original announcement was here :
BAM files first appeared in ensembl release 70 (were available till Ensembl release 78 at least):

If you just want to query/browse specific genes for tissues you can do that here:

This link has the tissue specific gene expression analysis from the bodymap data:
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Old 11-21-2015, 07:34 AM   #4
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thank you, I've been looking for a way to get already aligned bam files. I have access to the university's linux cluster but I don't have the time anymore to map. My PI wants this data asap. I've tried using these expression sites to find expression of my gene, but I am looking for a specific Isoform and there isn't a lot of information on it in the databases. Thank you again for a link to the already aligned bam files. Would you happen to know if these alignments are already "sorted"? Also they say they aligned them to the genome using the epstein barr virus as a decoy, do you know what that means?

Last edited by fk566938; 11-21-2015 at 07:39 AM.
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Old 11-21-2015, 11:50 AM   #5
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Originally Posted by fk566938 View Post
I have access to the university's linux cluster but I don't have the time anymore to map. My PI wants this data asap.
Your PI is underestimating the amount of training and effort it takes to get correct and useful results using bioinformatics. It's not just something you can toss in at the end on a whim.
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illumina, rnaseq, rnaseq alignment, tophat, tophat 2

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