Trinity transcriptome assembly

Question

[danvoronov]

Hi, Sorry, does anyone know if it is possible to run Trinity de-novo assembly using both FASTA and FASTQ files as input? Thanks. Best, Dan

Answer 1

[h.mon]

No, but you can convert the fastq files to fasta (or the fasta to fastq) with reformat.sh from BBTools, then use all files. If some of them are stranded and some unstranded, you should not set --SS_lib_type, and if the insert sizes are very different, you should set --group_pairs_distance according to the largest insert size.