Aligning Reads to Transcriptome Question

Question

[nikelle.petrillo]

Hello,

I would like to align my reads to the de novo transcriptome I created using Trinity. I am going to use trinity's "align_and_estimate_abundance.pl" to align. When I am putting together a code, can i use a concatenated file of all of left reads and a concatenated file of all my right reads? or do i need to put these individual files in my code separately, such as:

perl align_and_estimate_abundance.pl --transcripts /home/richardsonlab/AMMA_transcripts/updated36samplestrinityassembly/Trinity.fasta --seqType fq --left /home/npetrill/Trimmomatic-0-3.35/pairedoutput1 /home/npetrill/Trimmomatic-0-3.35/pairedoutput1a --right /home/npetrill/Trimmomatic-0-3.35/pairedoutput2 /home/npetrill/Trimmomatic-0-3.35/pairedoutput2a --est_method RSEM --aln_method bowtie --trinity_mode --output_dir /home/npetrill/aligning/--prep_reference

If i were to put in each file separately, do i need to use commas to separate?

Thanks for the help! Nikelle

[st.ph.n]

Did you combine multiple samples to make the assembly? If so, and you're going to do downstream DE analysis, align the raw reads from each sample independently. This will give you abundance estimates per sample in which to combine to a raw counts matrix. Then you can run any DE analysis software supported by Trinity, to get the DE results per comparisons.