Question: DE NOVO TRANSCRIPTOME AND COUNT
0
gravatar for ajmaninisha
2.3 years ago by
ajmaninisha30
Canada
ajmaninisha30 wrote:

Hi,

 

I used STAR to assemble contigs for de novo transcriptomics data and used the following pipeline:

Assemble the reads by Star ---> use the assemble contigs as refernce and then map it to samples -->  convert this sam file to fasta and blast it against own database to get the annoatations --->get the read count for mapped reads ---> and use edge R 

Kindly advice am i using the right approach?

1) There are a number of discussions regarding counting reads for de novo assembly which one is the best ? cant i use htseq but that requires a gtf file .

 

Please suggest

 

Thanks

ADD COMMENTlink modified 2.3 years ago by Jennifer Hillman Jackson24k • written 2.3 years ago by ajmaninisha30
0
gravatar for Jennifer Hillman Jackson
2.3 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Maybe try RSEM? It is available in the Galaxy Tool Shed.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.3 years ago by Jennifer Hillman Jackson24k
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