How can I get the information about NGS align information?

Question

[lee.jingu0626]

Hi.

I want to know how can I get the information about NGS align information.

For example, I want to get the information like this,

---

sample                                                                      S1        S2       S3       S4      S5      .....

exon_count                                                               0000      000    0000    0000   0000
exon_total_length
sequence_total_read
sequence_total_base
genome_aligned_read_random
genome_aligned_base_random
genome_aligned_read_unique
genome_aligned_base_unique
exon_aligned_read_random
exon_aligned_base_random
exon_aligned_read_unique
exon_aligned_base_unique
total_coverage(X)
genome_aligned_pct_base(genome_random/raw)
exon_aligned_pct_read(exon_random/raw)
exon_aligned_pct_base(exon_random/raw)
exon_aligned_pct_read(exon_random/genome_random)
exon_aligned_pct_base(exon_random/genome_random)
exon_aligned_pct_read(exon_unique/genome_unique)
exon_aligned_pct_base(exon_unique/genome_unique)

---

Samples (S1, S2, S3, S4, S5) are whole exome sequencing sample made by NGS.

Please recommend methods or software.

Answer 1

[GouthamAtla]

First you should tell what do u mean by each field like "genome_aligned_read_random" etc. A quick search gave me this paper and I guess you are referring to the tables from that paper.

[lee.jingu0626]

Actually, it is not necessary to get all field in that example. I just want to know the information about read alignment quality in sample such as exon count, total length of exon, total number of aligned read, total coverage, and read depth.

So please recommend some software to get this information.

Answer 2

[GouthamAtla]

samtools for manipulating sam/bam files and to get alignment statistics.

DEXSeq (HTSeq) provides scripts to remove the redundancy in the Ensemble GTF and get exon level counts.

bedtools for coverage statistics across genome or defined intervals.