Sequence and annotation information associated with genomic sequencing of QPX
Note- similar second digit in version indicates consistent naming structure
QPX_v0.1.7
CLC v5.1 Mismatch cost = 2; Perform scaffolding = Yes; Mapping mode = Map reads back to contigs (slow); Deletion cost = 3; Similarity fraction = 0.9; Length fraction = 0.8; Insertion cost = 3; Update contigs = Yes; Automatic word size = Yes; Minimum contig length =
10000; Automatic bubble size = Yes; input: filtered_QPX_DNA_GTGAAA_L001_R1 trimmed
Same naming structure as v0.1.5
Sequence
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FASTA
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555 sequences
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Annotation
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GFF
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Transcriptome BLAST against Genome
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Annotation
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SNP Locations (GFF)
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Annotation
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SNP Locations (BED)
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Annotation
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CG Locations (GFF)
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CG Locations (only + strand)
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Annotation
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Blast Hit Table
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SP tblastn v017; evalue 1E-40 -max_target_seqs 2
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Annotation
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GFF
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SP tblastn v017; evalue 1E-40 -max_target_seqs 2
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Annotation
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Blast Hit Table
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Physo3AA tblastn to v017; -evalue 1E-40 -max_target_seqs 10
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Annotation
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GFF
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Physo3AA tblastn to v017; -evalue 1E-40 -max_target_seqs 10
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QPX_v0.1.6
CLC v5.1 Mismatch cost = 2; Perform scaffolding = Yes; Mapping mode = Map reads back to contigs (slow); Deletion cost = 3; Similarity fraction = 0.9; Length fraction = 0.8; Insertion cost = 3; Update contigs = Yes; Automatic word size = Yes; Minimum contig length =
1000; Automatic bubble size = Yes; input: filtered_QPX_DNA_GTGAAA_L001_R1 trimmed
Same naming structure as v0.1.5
Sequence
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FASTA
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6848 sequences
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QPX_v0.1.5
CLC v5.1 Mismatch cost = 2; Perform scaffolding = Yes; Mapping mode = Map reads back to contigs (slow); Deletion cost = 3; Similarity fraction = 0.9; Length fraction = 0.8; Insertion cost = 3; Update contigs = Yes; Automatic word size = Yes; Minimum contig length = 100; Automatic bubble size = Yes; input: filtered_QPX_DNA_GTGAAA_L001_R1 trimmed
Sequence
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FASTA
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21,280 sequences
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Statistics
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Assembly Report
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Generated in CLC; stats provided for >10k assembly also (v0.1.7)
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Annotation
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Blast Table
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Blastx Swiss Prot; evalue <1E-5; max 10 hits
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Annotation
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Blast Table
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Blastx Swiss Prot; evalue <1E-5; max 1 hit; with gene description
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Annotation
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Blast Table
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Blastn nt; evalue <1E-5; max 10 hits
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Annotation
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SNP Table
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SNP table (CLC)
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Transcriptome
QPX_Transcriptome v2.1
QPX_Transcriptome v2 ORFs; nucleotides between stop codons; minimum size 200.
Sequence
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FASTA
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11,774 sequences
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Annotation
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GFF
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Indicating entire sequence is CDS
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Annotation
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SNP Table
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SNP table (CLC) with NonSyn notation
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QPX_Transcriptome v2
Subset of version 1 (v1) that only includes sequences with e-value < 1E-20. Based on Swiss-Prot blastx output, all sequences are oriented 5' - 3'.
Sequence
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FASTA
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3,778 sequences
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Annotation
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GFF
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CpG Annotation
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Annotation
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Tab Delim Txt
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CpG Observed / Expected Ratio
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Annotation
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Blast Hit Table
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tab delimited text: blastx Swiss-Prot evalue limit = 1E-20
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QPX_Transcriptome v1
Sequence
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FASTA
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11,280 sequences
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Statistics
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Tab Delim Txt
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Sequence Length
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Statistics
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Tab Delim Txt
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Transcriptome Assembly Stats
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Annotation
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Blast Hit Table
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tab delimited text: blastx Swiss-Prot evalue limit = 1E-05
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Annotation
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Blast HIt Table
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tab delimited text: blastx Swiss-Prot evalue limit = 1E-20
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Annotation
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Blast Hit Table
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tab delimited text: blastn nt evalue limit = 1E-5, 1 hit
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Annotation
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Ref Map (SAM)
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RNAseq reads mapped to transcriptome
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Annotation
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SNP table
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SNP detection based on RNAseq mapped to trans_v1
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Annotation
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SNP table
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RNAseq mapped to trans_v1; limit: 2 variants; cleaned
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