analysis of deletion/insertion from mitochondria NGS data

Question

[illinois.ks]

Hello,

I am trying to map the human mitochondria genome and try to find large insertion/deletion (> larger than 10 bps). I have paired-end fastq file of mitochondria genome using NGS..

It is the first time for me to do it. Could you please let me know the procedure for it?

Maybe, I am thinking to download the mitochondria reference human genome. Using only this one (instead of whole genome references), use bowtie2 to map to the reference mitochondria genome., which leads to the bam file..

Than, using this bam file, what kind of program do I have to use to identify the large (>10bp) insertion and deletion.

Please help me with this!

Answer 1

[Fidel]

For a deletion compute the read coverage (use bamCoverage from deepTools for this using the option --missingDataAsZero=yes) and output the result as a bedgraph. Then look for the regions with zero coverage:

grep -P "\t0.0$" your_file.bg

However, since the mitochondria genome is very small, just load the BAM file into IGV or any other genome browser. By eye you could see the regions that have no coverage.

Detecting an insertion is more difficult. You can check for copy number variation (here is a list of tools for that).

[illinois.ks]

Thank you Fidel.

I have run bowtie2 to map the mitochondria gene.

In this case, I have used whole genome fasta file and gtf file. (I am not sure whether it is right or not. I meant that I have to use only the mitochondria genome instead of whole genome for mapping..)

Here is the result of bowtie2 mapping. Could you please confirm for this?

bowtie2 -x genome -1 1-WMT-S1_L001_R1_001.fastq -2 1-WMT S1_L001_R2_001.fastq -S 1-WMT.sam

  96885 (100.00%) were paired; of these:
    6399 (6.60%) aligned concordantly 0 times
    22208 (22.92%) aligned concordantly exactly 1 time
    68278 (70.47%) aligned concordantly >1 times
    ----
    6399 pairs aligned concordantly 0 times; of these:
      351 (5.49%) aligned discordantly 1 time
    ----
    6048 pairs aligned 0 times concordantly or discordantly; of these:
      12096 mates make up the pairs; of these:
        4277 (35.36%) aligned 0 times
        1980 (16.37%) aligned exactly 1 time
        5839 (48.27%) aligned >1 times
97.79% overall alignment rate

[illinois.ks]

.. duplicated post