Question: SNPs summaries/statistics from output of KisSplice/KisSplice2RefTranscriptome
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gravatar for TrentGenomics
27 days ago by
TrentGenomics20 wrote:

Hi everyone,

I've successfully run the KisSplice/KisSplice2RefTranscriptome workflow to call de novo SNPs from 4 samples.

The outputs are printed to large .tsv files.

Are there any program packages designed to work with TSV files, similar to VCFtools for VCF files? My experience is novice at best when using simple text editors, so I was hoping that there may be a general practice for working with KisSplice/KisSplice2RefTranscriptome outputs.

Here is a sample output from the mainOutput.tsv file:

Component_ID SNP_ID Is_in_CDS Query_coverage SNP_position Codon_1 Codon_2 Amino_acid_1 Amino_acid_2 Is_not_synonymous Bubble_is_aligned_on_multiple_comp Bubble_is_aligned_on_multiple_seq Possible_sequencing_error Allele_frequency Read_counts_variant_1 Read_counts_variant_2 Is_condition_specific c59969_g1_i3 bcc_9888|Cycle_0|Type_0a True 100.0 1073 AGC TGC S C True False True True 0.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_0|C2_0|C3_0|C4_0|C5_8|C6_4|C7_0|C8_0 C1_0|C2_1|C3_1|C4_0|C5_0|C6_0|C7_1|C8_3 True c59969_g1_i1 bcc_9888|Cycle_0|Type_0a True 100.0 1060 TCA TCT S S False False True True 0.0|0.0|0.0|0.0|100.0|100.0|0.0|0.0 C1_0|C2_0|C3_0|C4_0|C5_8|C6_4|C7_0|C8_0 C1_0|C2_1|C3_1|C4_0|C5_0|C6_0|C7_1|C8_3 True c65168_g1_i1 bcc_86313|Cycle_0|Type_0a True 100.0 1748 GAG GAA E E False False False False 100.0|100.0|100.0|100.0|0.0|100.0|0.0|0.0 C1_2|C2_4|C3_5|C4_3|C5_0|C6_3|C7_0|C8_0 C1_0|C2_0|C3_0|C4_0|C5_0|C6_0|C7_15|C8_13 True c59737_g1_i3 bcc_86190|Cycle_69|Type_0a True 100.0 262 CTT CTC L L False False True False 0.0|0.0|100.0|100.0|0.0|100.0|0.0|100.0

Any info would be great! Thanks.

kissplice rna-seq snp • 153 views
ADD COMMENTlink modified 26 days ago • written 27 days ago by TrentGenomics20
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gravatar for TrentGenomics
26 days ago by
TrentGenomics20 wrote:

Spent the day learning awk and I think I may be alright with the post analysis.

ADD COMMENTlink written 26 days ago by TrentGenomics20
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