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Forum: RNA Sequencing 03-07-2016, 11:57 AM
Replies: 0
Views: 1,638
Posted By moldach
Red face On #IAmAResearchParasite, professional development and various RNA-Seq pipelines

Having just graduated with a M.Sc. I've got some free-time I would like to dedicate to learning some new bioinformatics software.

RNA-seq can give many views of biology depending on the pipeline:...
Forum: RNA Sequencing 03-07-2016, 11:16 AM
Replies: 8
Views: 2,845
Posted By moldach
Can anyone help?

Can anyone help?
Forum: RNA Sequencing 03-03-2016, 11:44 AM
Replies: 8
Views: 2,845
Posted By moldach
I had tried mapping at one point some-time-ago to...

I had tried mapping at one point some-time-ago to the closely related un-annotated genome. Unfortunately, I used Bowtie2. I now know better; you need to use a splice-junction aware aligner.



So...
Forum: RNA Sequencing 03-03-2016, 11:06 AM
Replies: 8
Views: 2,845
Posted By moldach
I mapped directly on my transcription assembly. ...

I mapped directly on my transcription assembly.

I couldn't find any reference to getting the number of reads on each transcript (maybe it's just worded differently?) from the documentation of...
Forum: RNA Sequencing 03-02-2016, 09:45 PM
Replies: 8
Views: 2,845
Posted By moldach
Assigning reads to genes in the absence of genomic annotation

I'm looking for a method to calculate read counts from SAM/BAM files that does not require an annotation file (GTF or BED files).

I've done a de novo transcriptome assembly of an organism which...
Forum: Bioinformatics 02-08-2016, 05:10 PM
Replies: 9
Views: 2,778
Posted By moldach
Thank you very much Genomax and Markiyan for your...

Thank you very much Genomax and Markiyan for your time and valuable feedback.
Forum: Bioinformatics 02-08-2016, 02:43 PM
Replies: 9
Views: 2,778
Posted By moldach
I used HiSeq250 Paired-end reads, this was...

I used HiSeq250 Paired-end reads, this was contracted out by BGI Hong Kong (unfortunately the details of their library prep aren't available so I'm not sure what fragment size of cDNA library they...
Forum: Bioinformatics 02-03-2016, 09:16 AM
Replies: 9
Views: 2,778
Posted By moldach
I have not done searches against the annotated...

I have not done searches against the annotated transcriptome with blastn. What exactly needs to be done when doing a blastn in addition to a blastx search? Would you just concatenate the resulting...
Forum: Bioinformatics 02-01-2016, 11:16 AM
Replies: 9
Views: 2,778
Posted By moldach
More information

Hi Genomax,

I am working with a diploid eukaryotic transcriptome (not genome) from a coral species in the Acropora spp. complex.

There is another Acropora species which there is an available...
Forum: Bioinformatics 02-01-2016, 09:03 AM
Replies: 9
Views: 2,778
Posted By moldach
Selecting the best database for blasting

Dear colleagues,

I recently asked a laboratory how they extended annotations on a transcriptome for a non-model organism; they pointed me towards their github.

Now this assembly/annotation...
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