Clarification on HW

[Ellior2]

To find a gene in our target organism that is also differentially expressed in a sea star with wasting disease, are we running blastx using a seastar transcriptome as a database and our query as our target organism? I found a contigs fasta file for a seastar that has had sea star wasting syndrome (Patiria miniata) on Echinobase and I found a C.gigas transcriptome fasta file on figshare

I tried blastx, but I keep ending up with a blank text file. Can you provide a little more direction or clarification?

[sr320]

Great question! Couple things 1) provide a url to what you are doing to better troubleshoot 2) comparing two nucleotides sequences is blastn

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Also you would only want to use the sea star seqs that are differentially expressed. Determined by using DESeq2 in R. Then use those seqs to compare to gigas (just use the proteome you are working with) That would be blastx

[mmiddleton]

I am having a hard time with that part as well... I got through the R part okay and ended up with the Phel_DEGlist.tab file, but now I'm confused about how to blast that since there aren't any sequences in that file, just the contig names (unless I understand less than I thought that I did, which is highly probable). Should we be getting a different file out of the repo and blasting that?

[yaaminiv]

I have a similar question to @mmiddleton !

I tried using the Phel_DEGlist.tab file as a database, but got the following error:

Is there a different FASTA file we should be using as a database instead?

And another question: I'm comparing .fastq files to the seastar genes. Does this mean I'm doing a blastn?

[laurahspencer]

I third this question; I had previously assumed that the next step was to use R to merge the Phel_DEGlist.tab file with our file (in my case I use the geoduck transcriptome file). However, since there are only contig names, which I don't believe have a standard naming convention based on bp sequence, i'm unsure how to move forward. Unless ... ... Do we retrace our steps using the contig names to determine the contig sequences (from original fasta file), then blast subsetted sea star fasta against our fasta? If so, I would guess that we can do this in R.

[sr320]

Think about it this way- what do you need to move forward?

On Wed, Oct 26, 2016 at 11:36 PM laurahspencer notifications@github.com wrote:

I third this question; I had previously assumed that the next step was to use R to merge the Phel_DEGlist.tab file with our file (in my case I use the geoduck transcriptome file). However, since there are only contig names, which I don't believe have a standard naming convention based on bp sequence, i'm unsure how to move forward. Unless ... ... Do we retrace our steps using the contig names to determine the contig sequences (from original fasta file), then blast subsetted sea star fasta against our fasta? If so, I would guess that we can do this in R.

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[sr320]

You are doing it exactly correct..

How would one take that list and get sequence info? Hint: look at the files in the eimd-sswd repo. What would you need to do?

On Wed, Oct 26, 2016 at 2:54 PM mmiddleton notifications@github.com wrote:

I am having a hard time with that part as well... I got through the R part okay and ended up with the Phel_DEGlist.tab file, but now I'm confused about how to blast that since there aren't any sequences in that file, just the contig names (unless I understand less than I thought that I did, which is highly probable). Should we be getting a different file out of the repo and blasting that?

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