Hi
I am aligning the paired exome sequencing data, that originated from
Sorted raw data bam file -->
Converted to fastq -->
Trimmed for adapters and quality -->
Alignment using bowtie2.
I get only 0.03% and 0.01% reads aligned concordantly >=1 times. Is there any way I can improve the alignment ? I would appreciate comments.
The following is the full alignment summary:
50608141 reads; of these:
50608141 (100.00%) were paired; of these:
50591535 (99.97%) aligned concordantly 0 times
14032 (0.03%) aligned concordantly exactly 1 time
2574 (0.01%) aligned concordantly >1 times
----
50591535 pairs aligned concordantly 0 times; of these:
86964 (0.17%) aligned discordantly 1 time
----
50504571 pairs aligned 0 times concordantly or discordantly; of these:
101009142 mates make up the pairs; of these:
50807764 (50.30%) aligned 0 times
45905252 (45.45%) aligned exactly 1 time
4296126 (4.25%) aligned >1 times
49.80% overall alignment rate
I am aligning the paired exome sequencing data, that originated from
Sorted raw data bam file -->
Converted to fastq -->
Trimmed for adapters and quality -->
Alignment using bowtie2.
I get only 0.03% and 0.01% reads aligned concordantly >=1 times. Is there any way I can improve the alignment ? I would appreciate comments.
The following is the full alignment summary:
50608141 reads; of these:
50608141 (100.00%) were paired; of these:
50591535 (99.97%) aligned concordantly 0 times
14032 (0.03%) aligned concordantly exactly 1 time
2574 (0.01%) aligned concordantly >1 times
----
50591535 pairs aligned concordantly 0 times; of these:
86964 (0.17%) aligned discordantly 1 time
----
50504571 pairs aligned 0 times concordantly or discordantly; of these:
101009142 mates make up the pairs; of these:
50807764 (50.30%) aligned 0 times
45905252 (45.45%) aligned exactly 1 time
4296126 (4.25%) aligned >1 times
49.80% overall alignment rate
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