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Old 08-24-2020, 11:32 AM   #1
Kaskere
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Location: Europe

Join Date: Jul 2018
Posts: 6
Default bwa alignement

Hello,
I am trying to align viral RNA sequences against reference fasta file.
It looks like it is not working properly

my index code looks like that

./bwa index reference.fasta

but I keep getting output like

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M:rocess] read 136386 sequences (10000131 bp)...
[M:rocess] read 136392 sequences (10000087 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 24370, 7, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (138, 175, 224)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 396)
[M::mem_pestat] mean and std.dev: (186.45, 62.40)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 482)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 136386 reads in 3.278 CPU sec, 3.070 real sec

Should I include options like -p and -a? I have no idea what exactly should be written in "Prefix of the output database" after index command
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Old 08-24-2020, 11:54 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

What is not working properly? Indexing genome and alignment are two independent steps. You completed the indexing of the genome. Now you need to align using `bwa mem`+ this index + your reads => Aligned SAM file => Aligned BAM file.

You could give your database a name that is what the "prefix" refers to. If you don't provide a name then your index is going to use the same "basename" as your reference file. In this case, "reference.fasta".
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