Multiple fastq for Trinity

Question

[bdeonovic]

When inputting multiple fastq files for Trinity do you put spaces or commas between the file names? The documentation says

 Required:
#
#  --seqType <string>      :type of reads: ( fa, or fq )
#
#  --JM <string>            :(Jellyfish Memory) number of GB of system memory to use for
#                            k-mer counting by jellyfish  (eg. 10G) *include the 'G' char
#
#  If paired reads:
#      --left  <string>    :left reads, one or more (separated by space)
#      --right <string>    :right reads, one or more (separated by space)
#
#  Or, if unpaired reads:
#      --single <string>   :single reads, one or more (note, if single file contains pairs, can use flag: --run_as_paired )

However, in their example they have

If you have multiple sets of fastq files, such as corresponding to multiple tissue types or conditions, etc., you can indicate them to Trinity like so:

Trinity --seqType fq --JM 50G  --left condA_1.fq,condB_1.fq,condC_1.fq --right condA_2.fq,condB_2.fq,condC_2.fq --CPU 6

Answer 1

[h.mon]

Which version of Trinity are you using? Are you reading the help online or at the command-line? Here is a copy/paste of the relevant help snippet after "Trinity --help" for Trinity 2.0.6:

#  If paired reads:
#      --left  <string>    :left reads, one or more file names (separated by commas, no spaces)
#      --right <string>    :right reads, one or more file names (separated by commas, no spaces)

edit: however, here is Trinity r20140413p1:

#  If paired reads:
#      --left  <string>    :left reads, one or more (separated by space)
#      --right <string>    :right reads, one or more (separated by space)

Probably the documentation went out of sync at some point, but for recent versions you should use commas.

Answer 2

[arnstrm]

The best way is to combine all R1 reads together, all R2 reads together and then use --left and --right options to supply input for Trinity (as shown in your example). If you have enough reads for each condition, then you can run Trinity separately on reads of each condition (pooling replicates).