Question: RNAseq data mapping to reference genome
0
gravatar for paulinefontaine87
3.1 years ago by
United States
paulinefontaine8710 wrote:

Hello,

I have some RNAseq Illumina fastq data. I would like to align it to the referece genome of c. elegans ce10. I have been struggling trying to do it in Galaxy.

Can you tell me what steps to do in order to get my VCF files and do so?

Thank you,

PF

rna-seq tophat bowtie • 1.2k views
ADD COMMENTlink modified 2.9 years ago by Guy Reeves1.0k • written 3.1 years ago by paulinefontaine8710
1
gravatar for paulinefontaine87
3.1 years ago by
United States
paulinefontaine8710 wrote:

Thank you Guy, that really help.

Now the only thing is I can't seem to select my region of interest on chromosome III (Region Chromosome, Start and end). Is it case sensitive maybe?

Thanks,

PF

 

 

ADD COMMENTlink written 3.1 years ago by paulinefontaine8710
0
gravatar for Guy Reeves
3.1 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

Hi PF 

Maybe: Groomer> BWA mem (select ce10 as reference from drop down menu)>freebayes =vcf of positions which  have some probability of differing from the reference .

All of these tools can be found by using the 'search tools' box in the  upper left part of the tools menu.

Not sure this is what you want from RNaseq but it is one of the quickest route to a vcf file.

Thanks Guy

 

ADD COMMENTlink written 3.1 years ago by Guy Reeves1.0k
0
gravatar for Guy Reeves
3.1 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

HI PF 

Yes it is case sensitive,  it will be 'chrIII'.  Using the the tools>Get data>UCSC Main

You should be able to get a BED file (which you can import to galaxy-see check box, or just view on the screen) with all the information you need 

chrIII:1-13783700

This look like the info you need but it may need to be in a different format some tools.

Thanks Guy

ADD COMMENTlink written 3.1 years ago by Guy Reeves1.0k
0
gravatar for paulinefontaine87
3.0 years ago by
United States
paulinefontaine8710 wrote:

Hello Guy,

Now that I have all my Freebayes VCF files, I can see some "alterations" to the reference genome in them. However do you how I can find out whether this alteration is:

- located in an exon or intron?

- the number of reads that have this alteration?

- changing the codon?

Or more generally, how do I interpret it

Thanks a lot in advance for your help,

PF

ADD COMMENTlink written 3.0 years ago by paulinefontaine8710
0
gravatar for Guy Reeves
2.9 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

HI 

In case you were still looking for an answer I would sugest you look at the tool snpEff  the documentation for which is explained in this link 

 http://snpEff.sourceforge.net

I will work with C.elegans 

Guy

ADD COMMENTlink written 2.9 years ago by Guy Reeves1.0k
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