bwa alignement

Kaskere · 08-24-2020, 11:32 AM

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

GenoMax · 08-24-2020, 11:54 AM

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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08-24-2020, 11:32 AM	#1
Kaskere Junior Member Location: Europe Join Date: Jul 2018 Posts: 6	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

08-24-2020, 11:54 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,090	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".