How to use samtools faidx
Hello everyone,
I would like to do a blast and then use the samtools faidx command in order to extract and align the hits from my blast. However, samtools faidx use an input in fasta format. My blast output is a text file.
Can someone help me ? Is there a way to convert a text file in fasta ? Thanks in advance
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florian.grosmaire •
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this is the wrong tool.
samtools faidx" indexes or queries regions from a fasta file ". For a start, you might use awk. For a very large file, import into a database.Thank you ! I understood where I was wrong . I will try something else. Instead of making a blast db I will try to make a biopython script that download sequences from ID's of the hits I get from my blast ouput
Align to a reference? To each other like doing a multiple sequence alignment? As discussed in your recent thread
blastdbcmdis appropriate to retrieve sequences from a blast database for further analysis.Thank you for your time and anwers !