Dear Biostars, Hi
Imagine that we have used RNA-seq approach in order to analyze the expression pattern of male and female gonad transcriptome of a non-model vertebrate (3 males and 3 females as biological replications- Illumina HighSeq paired-end).
Q: Is it possible to find any sex specific SNPs from this data using some tools or software ? How ?
NOTE1: It is a de novo project so no reference genome (or even close related) is available.
NOTE2: there are several isoforms for each transcripts in Trinity assembly that they are some times different in a few base pairs
for better understanding I have shown the SNP result ([]) for just one gene/transcripts with 11 isoform that I have gained from QualitySNPng softwar for both sex:
TRINITY_DN109863_c0_g1_i1,"408","TTCATGAAGATGACAGAGGACCAGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCG" TRINITY_DN109863_c0_g1_i1,"465","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACA" TRINITY_DN109863_c0_g1_i1,"576","TTCAAAAAAGAGGGCGATGATGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGCT" TRINITY_DN109863_c0_g1_i1,"993","TCACCCACTGCGATCTTCAAAGCGCTGCAACAGGCCGATTCCCCTCACTC[T/C]GCGTCCAGCATGAGC" TRINITY_DN109863_c0_g1_i1,"1137","CAGGCTGGAAAAGCAGACGAAACGGGAAGGGCGCCCCCTGCAGGAAGG[T/A]GGTGGCAGGCT" TRINITY_DN109863_c0_g1_i1,"1797","CACAGTCCTCAGCACTGGAGCAGCCTGTCTACACACAGCTCACCAGGCC[G/T]TAGGAGCCATTCA" TRINITY_DN109863_c0_g1_i10,"408","TTCATGAAGATGACAGAGACCAGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCG" TRINITY_DN109863_c0_g1_i10,"465","ATGTCCGAGGATTCTGCGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAA" TRINITY_DN109863_c0_g1_i10,"576","TTCAAAAAAGAGGGCGATGATGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGCGT" TRINITY_DN109863_c0_g1_i10,"993","TCACCCACTGCGATCTTCAAAGGCTGCAACAGGCCGATTCCCCTCACTC[T/C]GCGTCCAGCATGACAGTC" TRINITY_DN109863_c0_g1_i10,"1137","CAGGCTGGAAAAGCAGATCTAAACGGGAAGGGCGCCCCCTGCAGGAAGG[T/A]GGTGGCAGGCAGAGCT" TRINITY_DN109863_c0_g1_i11,"407","TTCATGAAGATGACAGAGGACAGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCGAGG" TRINITY_DN109863_c0_g1_i11,"464","ATGTCCGAGGATTCTGCGGGGTCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACCCAGTCA" TRINITY_DN109863_c0_g1_i11,"575","TTCAAAAAAGAGGGCGATGATGCAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGCTGCCCGT" TRINITY_DN109863_c0_g1_i11,"1139","CCTGGAAAAGCAGATCTGAACGGGAAGGGCGCCCCCTGCAGGAAGGAGG[T/C]GGCAGGCAGCAGAGCTGAG" TRINITY_DN109863_c0_g1_i11,"1796","CACAGTCCTCAGCACTGGGACAGCCTGTCTACACACAGCTCACCAGGCC[G/T]TAGGAGCCATTCCC" TRINITY_DN109863_c0_g1_i12,"408","TTCATGAAGATGACAGAGGACCGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCGGATCGGG" TRINITY_DN109863_c0_g1_i12,"465","ATGTCCGAGGATTCTGCGGGGTCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACGTCA" TRINITY_DN109863_c0_g1_i12,"576","TTCAAAAAAGAGGGCGATGATGCAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGCGT" TRINITY_DN109863_c0_g1_i12,"993","TCACCCACTGCGATCTTCAAAGGCTGCAACAGGCCGATTCCCCTCACTC[T/C]GCGTCCAGCATGAGCAGTC" TRINITY_DN109863_c0_g1_i12,"1137","CAGGCTGGAAAAGCAGATCTGAACGGGAAGGGCGCCCCCTGCAGGAAGG[T/A]GGTGGCTGGAGAGCT" TRINITY_DN109863_c0_g1_i2,"407","TTCATGAAGATGACAGAGGACCAGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCGTCTGGATCGGG" TRINITY_DN109863_c0_g1_i2,"464","ATGTCCGAGGATTCTGCGGGGTCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACCAGACAGTCA" TRINITY_DN109863_c0_g1_i2,"575","TTCAAAAAAGAGGGCGATGATGAAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGCTGAACCGT" TRINITY_DN109863_c0_g1_i2,"1136","CAGGCTGGAAAAGCAGATCTGAACGGGAAGGGCGCCCCCTGCAGGAAGG[T/A]GGTGGAGCAGCCGGAGAGCT" TRINITY_DN109863_c0_g1_i2,"1796","CACAGTCCTCAGCACTGGGAGCGCCTGTCTACACACAGCTCACCAGGCC[G/T]TAGGAGCCATTCAGACCATCCC" TRINITY_DN109863_c0_g1_i3,"437","TTCATGAAGATGACAGAGGACCAGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCCTGGATCGGG" TRINITY_DN109863_c0_g1_i3,"494","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACA" TRINITY_DN109863_c0_g1_i3,"605","TTCAAAAAAGAGGGCGATGATGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGCCGT" TRINITY_DN109863_c0_g1_i3,"1022","TCACCCACTGCGATCTTCAAAGCGCTGCAACAGGCCGATTCCCCTCACTC[T/C]GCGTCCAGCAGTC" TRINITY_DN109863_c0_g1_i3,"1166","CAGGCTGGAAAAGCAGATCTGAAACGGGAAGGGCGCCCCCTGCAGGAAGG[T/A]GGTGGCAGGCACT" TRINITY_DN109863_c0_g1_i4,"437","TTCATGAAGATGACAGAGGACCAGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCGGG" TRINITY_DN109863_c0_g1_i4,"494","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAAACAGTCA" TRINITY_DN109863_c0_g1_i4,"605","TTCAAAAAAGAGGGCGATGATGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTCCCGT" TRINITY_DN109863_c0_g1_i4,"1022","TCACCCACTGCGATCTTCAAAGCGCTGCAACAGGCCGATTCCCCTCACTC[T/C]GCGTCCAGCATGAGCCCAGTC" TRINITY_DN109863_c0_g1_i4,"1166","CAGGCTGGAAAAGCAGATCTGAAACGGGAAGGGCGCCCCCTGCAGGAAGG[T/A]GGTGGCAGGCAGCT" TRINITY_DN109863_c0_g1_i5,"407","TTCATGAAGATGACAGAGGACCAGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCTGGATCGGG" TRINITY_DN109863_c0_g1_i5,"464","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACCAGACAGTCA" TRINITY_DN109863_c0_g1_i5,"575","TTCAAAAAAGAGGGCGATGATGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGCCCGT" TRINITY_DN109863_c0_g1_i5,"1139","CCTGGAAAAGCAGATCTGAAGCGGGAAGGGCGCCCCAGGAAGGAGG[T/C]GGCAGGCAGCGCTGAG" TRINITY_DN109863_c0_g1_i6,"464","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACAA" TRINITY_DN109863_c0_g1_i6,"575","TTCAAAAAAGAGGGCGATGAGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGGT" TRINITY_DN109863_c0_g1_i6,"1139","CCTGGAAAAGCAGATCTGAAGCGGGAAGGGCGCCCCCTGCAGGAAGGAGG[T/C]GGCAGGCAGCCTTGAG" TRINITY_DN109863_c0_g1_i7,"435","TTCATGAAGATGACAGAGGACCGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCGAGATCGGG" TRINITY_DN109863_c0_g1_i7,"492","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACCAGAGTCA" TRINITY_DN109863_c0_g1_i7,"603","TTCAAAAAAGAGGGCGATGATGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGT" TRINITY_DN109863_c0_g1_i7,"1020","TCACCCACTGCGATCTTCAAAGGCTGCAACAGGCCGATTCCCCTCACTC[T/C]GCGTCCAGCAC" TRINITY_DN109863_c0_g1_i7,"1425","GTCCCCCAAGCAGCAAACGTCGCGGGGCACGCTTGGATGGCCAAGCAGCA[A/G]CAGCAGCAGCA" TRINITY_DN109863_c0_g1_i8,"408","TTCATGAAGATGACAGAGGACCGGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGG" TRINITY_DN109863_c0_g1_i8,"465","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACCAGTCA" TRINITY_DN109863_c0_g1_i8,"576","TTCAAAAAAGAGGGCGATGTGACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGGTGGT" TRINITY_DN109863_c0_g1_i8,"1140","CCTGGAAAAGCAGATCTGAGCGGGAAGGGCGCCCCCTGCAGGAAGGAGG[T/C]GGCAGGCAGCCTGAG" TRINITY_DN109863_c0_g1_i8,"1797","CACAGTCCTCAGCACTAGCAGCCTGTCTACACACAGCTCACCAGGCC[G/T]TAGGAGCCATTCAGAATGCCATCCC" TRINITY_DN109863_c0_g1_i9,"437","TTCATGAAGATGACAGAGGACCGAGAAATGTCTGTCAGACGCCCCCAG[C/T]CCGAGCATGTCCGAGGGATCGGG" TRINITY_DN109863_c0_g1_i9,"494","ATGTCCGAGGATTCTGCGGGGTCCCCGTGCCCGTCTGGATCGGGCTCCGA[T/C]GCTGAGAACACCACGGACAGTCA" TRINITY_DN109863_c0_g1_i9,"605","TTCAAAAAAGAGGGCGATGATACAAATTCCCCGTTTGCATCAGGGATGC[T/G]GTTTCCCAGCCCGT" TRINITY_DN109863_c0_g1_i9,"1022","TCACCCACTGCGATCTTCAAGCGCTGCAACAGGCCGATTCCCCTCACTC[T/C]GCGTCCAGCATGAGTC" TRINITY_DN109863_c0_g1_i9,"1166","CAGGCTGGAAAAGCAGATCTGAAAGGGAAGGGCGCCCCCTGCAGGAAGG[T/A]GGTGGCAGGCAATTGGAGAGCT" TRINITY_DN109863_c0_g1_i9,"1826","CACAGTCCTCAGCACTGGAGCAGCCTGTCTACACACAGCTCACCAGGCC[G/T]TAGGAGCCAATCCC"
Thank you in advance
Does that even make sense to look for sex specific SNPs? The only locus you can find those are the sex chromosomes and then the zygosity is most informative. But perhaps I miss something important about your organisms, forgive me my ignorance about fish genetics.
Hi @Wouter and Happy New Year!
Most fishes have not sex chromosomes.
I was thinking that is it even practical to search for SNPs in males and females of the same species ? and what is the standard pipeline for it ?
~ take care
Happy New Year to you too! See, I wasn't aware that fish do not have sex chromosomes. But would it even make sense to find gender-specific SNPs then? You might by chance find SNPs which are present only in one of both sexes, but that finding will not be generalized to a broader population of fish.
I guess finding that SNPs is a project and proofing the existence of it in the population is another project. I intend to run the first one for now ;-).
NOTE: many fish has sexually dimorphic chromosomes, but most of the fishes has not.
But the other project doesn't make biological sense, why would SNPs be gender specific?
I don't know why! I will hunt it first and then check for its cause.
I have seen in many RNA-seq papers that they have report how many SNPs they have found. but If they are not as different as DEGs, what is the usage of such SNPs ?