Hi Albert,

As per your advice I used bwa-mem for alignment it work out very well. It think I got 79% align. Can you please check my flagstat output. If I am interpreting result in correct manner.

If it is 79% align can you please help me how can I improve alignment above 90% by adding more parameter.

I used following cmd:

##bwa index contigs.fa
##bwa mem contigs.fa CombineIonXpressRNA_009_NareshPool_Chip1_2_WT1_fastx_trimmer_from_quality_trimmer_file.fastq > aln-se.sam
##samtools view -bS aln-se.sam > aligned_reads.bam
##samtools flagstat aligned_reads.bam
34569162 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
27555361 + 0 mapped (79.71%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Appreciate your help.

Thanks,
Naresh