Reference for alignment

[maivantan]

Dear all,
I index a reference genome and try to align in bowtie2, i got the result. how ever, when i align using samtools by VCF format, the reference showed not available.

user$ ./bowtie2 -x ~/tan_analysis/rice1 -U ~/tan_analysis/analysis20140111/20140111_A1_PE1.fastq -S wrc20140118.sam
2398641 reads; of these:
2398641 (100.00%) were unpaired; of these:
2094522 (87.32%) aligned 0 times
228676 (9.53%) aligned exactly 1 time
75443 (3.15%) aligned >1 times
12.68% overall alignment rate

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT wrc20140118.sorted.bam.bam
chr01 27400 . N G 68 . DP=22;VDB=3.856020e-04;AF1=1;AC1=2;DP4=0,0,0,8;MQ=29;FQ=-51 GT:PL:GQ 1/1:101,24,0:45
chr01 27401 . N C,G 75 . DP=22;VDB=1.934810e-04;AF1=1;AC1=2;DP4=0,0,0,9;MQ=28;FQ=-51 GT:PL:GQ 1/1:108,24,0,104,10,101:45
chr

Do you have any suggestion please

[swbarnes2]

Two quick things to try:

First make sure that you really did use the same reference between Bowtie and samtools, and make sure that the chromosome names in the reference match the names in your .bam.

Then remake the .fai file yourself (use samtools faidx), then rerun samtools mpileup

[maivantan]

I used the same reference between bowtie2 and samtools.

I will try as your suggestion.

Thank you very much,