Hi, I used Blast and Trinotate to annote de novo assembly I constructed using Trinity.
Now, I want to study that transcripts without blast hit (they doesn't appear in the Trinotate output). My question is: How can I exctract that unmapped transcripts? Is there a way to tell blast to output the unmapped reads into a separate file?
I want do it because I'm studdying the presence of new Antimicrobial Peptide Genes in Blatella germanica (it doesn't have a reference genome).
Any advice or suggestion is welcome. Thanks in advance :)
2 answers
Is there a way to tell blast to output the unmapped reads into a separate file?
No there is not. You will need to use -outfmt 7 when you blast (which will include reads that do not map) and then pull out the id's of the reads that do not map. See: Blast - How to get the no hits result on table output?
Once you have the id's that do not map, you can use answer here to extract the reads from your query file: Extract fasta sequnces not matching a list
have a look at comm or join.
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join
extract the names of your queries, sort and save into 'a'. extract the names of the blast output and save into 'b'
'comm -23 a b' will show you the queries that were not found by blast.
Log in to answer this question.
-
How can I search for orthologs ?
written by D •
-
Aggregate isoforms to gene level after de novo transcriptome assembly.
written by Twitty •
-
Trinity transcriptome quality assessment
written by cwbenson1993 •
-
How to retain transcripts from blastx output at a given coverage?
written by unawaz •
-
Forum: Pipeline suggestions for GO & pathway analysis for species without reference genome
written by Whoknows
-
Is it right to merge different trinity transcript assembly of same plant ?
written by Mahendra Gaur •
-
How to map RNA-seq reads of a species to a reference genome of another close species ?
written by Farbod
-
assessing de novo Trinity assembly quality
written by trish0401 •
-
Local Blast against a specific organism
written by Ritvik •
-
Best Reciprocal BLAST and Alternative Transcripts
written by pld
