how to extract contigs from file and

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6.4 years ago

matiqau ▴ 10

Hello everyone, I am a beginner in the field of bioinformatics and my questions will be very basic.sorry about that. I have run trinity on RNA sample library got the trinity.fasta file. next i run blasx and got output.tx file and extract seq id .got ID LIST AND RUN FASTACMD and got ID-list.fasta file.This file has a long list of >gi number, protein, and various Viruses. i have got 160 >gi with different virus (some viruses correspond to 20 >gi or even greater. My Questions are 1) which command in Linux can be used to organize these viruses according to their >gi number. 2) how to extract contigs from these viruses >gi number.,as i want to run blastn keeping the Trinity.fasta as reference sequence contigs. Thanks

rna-seq alignment blast • 1.6k views

ADD COMMENT • link 6.4 years ago by matiqau ▴ 10

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Please post example input lines and expected output. It would be helpful to address OP issues.

ADD REPLY • link 6.4 years ago by cpad0112 21k

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