Question: What should I do if i want Stringtie to assemble mitochondrial transcripts?
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gravatar for pilyric
2.0 years ago by
pilyric0
pilyric0 wrote:

Hi, I'm working on some RNA-seq data, but when I tried to use Stringtie to assemble transcripts, some problem occured. It seems that Stringtie uses exon and CDS annotation to assemble transcripts, but there's no annotation containing exon information of mtDNA. There's no exons in mtDNA indeed, but if i want Stringtie does correct assembly, what should I do? thanks a lot

NC_005044.2 RefSeq CDS 2742 3697 . + 0 gene_id "1485856", transcript_id "TRANS.1130808", gene_name "ND1"

NC_005044.2 RefSeq CDS 3907 4948 . + 0 gene_id "1485857", transcript_id "TRANS.1130809", gene_name "ND2"

NC_005044.2 RefSeq CDS 5329 6873 . + 0 gene_id "1485858", transcript_id "TRANS.1130810", gene_name "COX1"

NC_005044.2 RefSeq CDS 7016 7699 . + 0 gene_id "1485859", transcript_id "TRANS.1130811", gene_name "COX2"

NC_005044.2 RefSeq CDS 7771 7968 . + 0 gene_id "1485860", transcript_id "TRANS.1130812", gene_name "ATP8"

NC_005044.2 RefSeq CDS 7929 8609 . + 0 gene_id "1485861", transcript_id "TRANS.1130813", gene_name "ATP6"

NC_005044.2 RefSeq CDS 8609 9392 . + 0 gene_id "1485862", transcript_id "TRANS.1130814", gene_name "COX3"

NC_005044.2 RefSeq CDS 9462 9807 . + 0 gene_id "1485863", transcript_id "TRANS.1130815", gene_name "ND3"

NC_005044.2 RefSeq CDS 9878 10174 . + 0 gene_id "1485864", transcript_id "TRANS.1130816", gene_name "ND4L"

NC_005044.2 RefSeq CDS 10168 11545 . + 0 gene_id "1485865", transcript_id "TRANS.1130817", gene_name "ND4"

NC_005044.2 RefSeq CDS 11748 13568 . + 0 gene_id "1485866", transcript_id "TRANS.1130818", gene_name "ND5"

NC_005044.2 RefSeq CDS 13552 14079 . - 0 gene_id "1485867", transcript_id "TRANS.1130819", gene_name "ND6"

NC_005044.2 RefSeq CDS 14153 15292 . + 0 gene_id "1485868", transcript_id "TRANS.1130820", gene_name "CYTB"

rna-seq assembly • 609 views
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