Question: problem converting indexed fasta file to SAM format using bowtie2
gravatar for jamessemaj712
3.5 years ago by
jamessemaj71210 wrote:


1)I downloaded asi_ref_ASM45574v1_chrMT.fa file from NCBI. 2)I created reads using wgsim using the following command: wgsim -N1000 -S1 asi_ref_ASM45574v1_chrMT.fa sim_reads.fq /dev/null

3)Then I created index file of the .fa file mentioned above by using the following command samtools faidx asi_ref_ASM45574v1_chrMT.fa

I got a asi_ref_ASM45574v1_chrMT.fa.fai

4)After this I tried to convert the .fai file to sam for further analysis but received an error. Here is the command bowtie2 -x asi_ref_ASM45574v1_chrMT.fa.fai -U sim_reads.fq -S sim_reads_aligned.sam

and here is the error: Could not locate a Bowtie index corresponding to basename "asi_ref_ASM45574v1_chrMT.fa.fai" Error: Encountered internal Bowtie 2 exception (#1) Command: /usr/bin/bowtie2-align-s --wrapper basic-0 -x asi_ref_ASM45574v1_chrMT.fa.fai -S sim_reads_aligned.sam -U sim_reads.fq (ERR): bowtie2-align exited with value 1

I am not understanding why the error.Where am I wrong?

snp sam fasta index bowtie2 • 1.1k views
ADD COMMENTlink modified 3.5 years ago by mastal5112.0k • written 3.5 years ago by jamessemaj71210

You need to index the fasta file using bowtie2-build:

bowtie2-build asi_ref_ASM45574v1_chrMT.fa asi_ref_ASM45574v1_chrMT

Then align using:

bowtie2 -x asi_ref_ASM45574v1_chrMT -U sim_reads.fq -S sim_reads_aligned.sam
ADD REPLYlink written 3.5 years ago by fanli.gcb690

Thanks.It works.But may I know why didn't samtols faidx not work?

ADD REPLYlink written 3.5 years ago by jamessemaj71210
gravatar for mastal511
3.5 years ago by
mastal5112.0k wrote:

The two types of index are different.

ADD COMMENTlink written 3.5 years ago by mastal5112.0k
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