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Extract Transcript sequence from fastq file (Plant RNA-Seq data)

I have a plant RNA-Seq data and I want to extract the transcript sequence of the some transcripts. How can I do that ??

rna-seq
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updated by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup • written by hafiz.talhamalik hafiz.talhamalik

You can extract transcript sequences directly from ensembl plants biomart, you don't need RNA-seq data for that. In case it is transgenic with fused transcripts or something like that, then you can use blast to extract reads from fastq file and then assemble them.

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written by ashish ashish

ok let me try that.. and any idea of tool for annotation of plant assembly ?

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written by hafiz.talhamalik hafiz.talhamalik

@ hafiz.talhamalik

Is this plant genome already sequenced and annotated? If so, go for reference based assembly (with reference sequence) and post alignment, you can extract transcripts (sequence) of interest using annotation file. For aligning RNAseq data, use splice aware aligners such as hisat2, star.

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written by cpad0112 cpad0112

yes it's known one Brassica Napus. I tried reference based assembly using trinity but assembly results were not good..!! any other good assembler ??

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written by hafiz.talhamalik hafiz.talhamalik

1 answer

If you have RNAseq you can also do a guided transcriptome assembly - basically look for transcripts in your data that does not appear in the annotation database - you can read more about considerations and tools here.

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written by Kristoffer Vitting-Seerup Kristoffer Vitting-Seerup

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