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kingsfordgroup / sailfish

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
http://www.cs.cmu.edu/~ckingsf/software/sailfish
GNU General Public License v3.0
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sailfish index -t does not take multiple transcript fasta file #98

Open jeremywzh opened 8 years ago

jeremywzh commented 8 years ago

Hi, I'm using v.0.10.0. sailfish index -t --help says "-t" can take Transcript fasta file(s). However when I try:

sailfish index -t gencode.vM9.pc_transcripts_txids.fa gencode.vM9.lncRNA_transcripts_txids.fa -o . or sailfish index -t gencode.vM9.pc_transcripts_txids.fa -t gencode.vM9.lncRNA_transcripts_txids.fa -o .

I got different index size if I manually combine gencode.vM9.pc_transcripts_txids.fa and gencode.vM9.lncRNA_transcripts_txids.fa into one fasta file and run:

sailfish index -t gencode.vM9.pc_lncRNA_transcripts_txids.fa -o .

rob-p commented 8 years ago

Hi Jeremy,

I apologize for the confusion. This is a bug in the documentation. If you want to index a set of transcripts from distinct files, the easiest thing to do is:

sailfish index -t <(cat gencode.vM9.pc_transcrits_txids.fa gencode.vM9.lncRNA_transcripts_txids.fa) -o .

Since sailfish can read from a streaming input file, this will concatenated the transcripts together "on the fly" without the need to make any intermediate files. I will update the documentation to reflect this.

--Rob