Trinity --SS_lib_type command

Question

[Princy]

Hello, I need to do Trinity. what should I write in --SS_lib_type or whether it is non-strand-specific reads. I have paired-end fastq files. Is SO_2861_PIT_trim_1P.fq file is forward and SO_2861_PIT_trim_2P.fq file is reverse? The first file looks like this.

 head Fish_Data-2/trinity_BR/SO_2861_PIT_trim_1P.fq
@MG00HS12:390:C3VVMACXX:7:1101:1571:1858 1:N:0:GTCCGC
NTCTGATATAACATTTCACATTGGTGCTAAGCGATTTATGGCAATATGATGTGGCCAAAATGACCTTAACAATATGTTCTAGTATATTATCGCTCAAAAAA
+
#1=DDDDDHAFHHIJJGIJJJJGIHHIJEHIIJHJGIGHJIJJGIHEBBHGIJJJJIIHIIJIJJJHGIIJIICHHE>?EHHBEFFFFFFEABEBDCC>A=
@MG00HS12:390:C3VVMACXX:7:1101:1746:1901 1:N:0:GTCCGC
NGACTACGTTATTGAAGAGCCGCTGGTTATCTGATGCTCTCCCCTGGTTCACCAACAAACTAACCAGCACCACCGACAACAGCACTAATGCTCTAGCCATT
+
#1=DDFFFHGHHHIIJIJJJJIIJIIJIGHGIBHGEHGGIIJCHIJIGHGIJIGIIIJJJIGHHHEFBEFDECDDDDDDDDDDDDDDDDDCACDDDDDCDD
@MG00HS12:390:C3VVMACXX:7:1101:1686:1920 1:N:0:GTCCGC
NTGATGTTGTAAACATTAGGTATGCAGGAAATAATGACTTTATTTTTTAAAAGAATGAACACTTGACCTTTAAATCATATTAAATGAATGTGCATATGTAG

2nd file looks like this

>  head Fish_Data-2/trinity_BR/SO_2861_PIT_trim_2P.fq
@MG00HS12:390:C3VVMACXX:7:1101:1571:1858 2:N:0:GTCCGC
ACTCGAGTGAACCCATCCATTTAGATTACAATTTCAACACTGATCTTAAGCCTTTTTTGAGCGATAATATACTAGAACATATTGTTAAGGTCATTTTGGCC
+
CCCFFFFDHHFHHJF>FHGHGEEDHHHHIIIJEHCFGI>DHIGDAFIIIGGFHIJJJJH@FIGJGHHDFFFFEFDCDEEEDDDEED@ACCAC@CEEEDBCD
@MG00HS12:390:C3VVMACXX:7:1101:1746:1901 2:N:0:GTCCGC
AAGAGTTTGTCTACCCTGAGCGAAATGGCTAGAGCATTAGTGCTGTTGTCGGTGGTGCTGGTTAGTTTGTTGGTGAACCAGGGGAGAGCATCAGATAACCA
+
BCCDFFFFHHGHHJJJJIGIJIIJIJJIIJJJGGGEGHH>?FEH<?FGHGFHAG<;DEHHIAEEB>;@@DFBCAB;@CB?ABBD8@<B?>CCCDCCCCDDC
@MG00HS12:390:C3VVMACXX:7:1101:1686:1920 2:N:0:GTCCGC
GAATATTCATTATGTTTCCATTTGCATCACAAATTGGCATTGTTGCAGAAAATGTCTGATCTCATTTTAAGGAGAGATACAAACTGTAGCCATAGACAGAA

[andres.firrincieli]

long story short, you should contact the person/facility that prepared the library and ask whether or not the library is strand-specific: link

[GenoMax]

To add a bit of clarification, if you don't have a reference genome available (likely here) then you will need to ask the provider that made the libraries. Otherwise infer_experiment.py from RSeQC or even salmon can be used (if you have a transcriptome available).