Hi All,
I am blasting my miRNA-seq fasta file against rFam data base. Here is the command line I used:
blastn -query TOTAL_mapped_reads.fa -task megablast -db Rfam.fasta -out mapped_vs_rfam.txt -outfmt "6 qseqid sseqid qlen evalue pident nident mismatch qcovs qcovhsp"
Then I want to retrive those reads which match tRNAs in rFam.
There are many hits in the output (see the attached picture).
But when I pick the first read which is shown to be 100% match with rRNA in rfam by searching it in rfam website, there is no hit.
>62-796337
TCCCATATGGTCTAGCGGTTAGGATTCCTGGTT
Briefly, according to my blast result against rfam database, there is a match, but when I search the my sequence in online rfam website, there is no hit. So what is the problem?
I am blasting my miRNA-seq fasta file against rFam data base. Here is the command line I used:
blastn -query TOTAL_mapped_reads.fa -task megablast -db Rfam.fasta -out mapped_vs_rfam.txt -outfmt "6 qseqid sseqid qlen evalue pident nident mismatch qcovs qcovhsp"
Then I want to retrive those reads which match tRNAs in rFam.
There are many hits in the output (see the attached picture).
But when I pick the first read which is shown to be 100% match with rRNA in rfam by searching it in rfam website, there is no hit.
>62-796337
TCCCATATGGTCTAGCGGTTAGGATTCCTGGTT
Briefly, according to my blast result against rfam database, there is a match, but when I search the my sequence in online rfam website, there is no hit. So what is the problem?
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