Burrows Wheeler Aligner - tool
Hi, I'm new to BWA tool. I indexed my reference.fa using command:
bwa index -a bwtsw reference.fa reference_prefix
and got 3 output files: .amb .ann .pac
I read that the above command must produce 8 output files such as .amb .ann .bwt .pac .rbwt .rpac .rsa .sa.
As only 3 output files have been generated, has the command run successfully? If not what should I do?
TIA
1 answer
Log in to answer this question.
More posts like this
-
RNA-seq: problems with DEcontamination with Deconseq
written by lam.black.rider •
-
bwa index with no .sa file
written by CaffeSospeso •
-
what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
written by lffu_0032
-
BWA indexer fails to generate fasta.sa file!
written by reza.jabal
-
Same BWA INDEX files for 0.7.12 and 0.7.13 versions?
written by vladimir.kovacevic
-
Use of Deconseq chromosome libraries
written by luigi.marongiu •
-
what is meaning of bwa index output
written by alexqdh •
-
Bwa Index Output And Bwa Aln Problem
written by Tonyzeng •
-
Do Different Versions Of Bwa Create Differently Named Index Files?
written by mathiasf52 •
-
Bwa Indexing
written by Kssr
bwa indexoutput some messages to the screen, what did they say?Hey, So the messages displayed are: 1. bwa_index Pack FASTA 2. Construct BWT for the packed sequence 3. BWT_gen 4. Update BWT 5. Pack forward only FASTA 6. Construct SA from BWT and Occ...
What is the reason that you chose
bwtsw?Hey, I chose bwtsw as the genome I'm analysing is of larger size, say 3.3 GB. Hence.