Workshop on Genomics (Week 2, Day 3) – Transcriptomics

Dr. Manual Garber:

Lecture slides: http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2013/03/evomics_krumlov_2014.pdf

Exercises: http://evomics.org/learning/genomics/transcriptomics/#part1

Exercise 1: Prepare for genomic alignment (when there is reference genome)
Exercise 2: Genome alignment of RNA-seq reads

Question: What percent of reads were mapped for each library?

ubuntu@ip-10-151-69-171:~/transcriptomics/tophat$ cat th.quant.ctrl1/align_summary.txt th.quant.ctrl2/align_summary.txt th.quant.ctrl3/align_summary.txt th.quant.expr1/align_summary.txt th.quant.expr2/align_summary.txt th.quant.expr3/align_summary.txt
Left reads:
          Input     :     24288
           Mapped   :     23768 (97.9% of input)
            of these:       511 ( 2.1%) have multiple alignments (65 have >20)
Right reads:
          Input     :     24288
           Mapped   :     23770 (97.9% of input)
            of these:       515 ( 2.2%) have multiple alignments (65 have >20)
97.9% overall read mapping rate.

Aligned pairs: 23746
of these: 505 ( 2.1%) have multiple alignments
442 ( 1.9%) are discordant alignments
95.9% concordant pair alignment rate.
Left reads:
Input : 15693
Mapped : 15181 (96.7% of input)
of these: 388 ( 2.6%) have multiple alignments (50 have >20)
Right reads:
Input : 15693
Mapped : 15164 (96.6% of input)
of these: 387 ( 2.6%) have multiple alignments (50 have >20)
96.7% overall read mapping rate.

Aligned pairs: 15143
of these: 381 ( 2.5%) have multiple alignments
286 ( 1.9%) are discordant alignments
94.7% concordant pair alignment rate.
Left reads:
Input : 17008
Mapped : 16497 (97.0% of input)
of these: 300 ( 1.8%) have multiple alignments (32 have >20)
Right reads:
Input : 17008
Mapped : 16500 (97.0% of input)
of these: 299 ( 1.8%) have multiple alignments (32 have >20)
97.0% overall read mapping rate.

Aligned pairs: 16478
of these: 295 ( 1.8%) have multiple alignments
270 ( 1.6%) are discordant alignments
95.3% concordant pair alignment rate.
Left reads:
Input : 17568
Mapped : 17068 (97.2% of input)
of these: 225 ( 1.3%) have multiple alignments (13 have >20)
Right reads:
Input : 17568
Mapped : 17070 (97.2% of input)
of these: 225 ( 1.3%) have multiple alignments (13 have >20)
97.2% overall read mapping rate.

Aligned pairs: 17047
of these: 223 ( 1.3%) have multiple alignments
185 ( 1.1%) are discordant alignments
96.0% concordant pair alignment rate.
Left reads:
Input : 21020
Mapped : 20497 (97.5% of input)
of these: 238 ( 1.2%) have multiple alignments (13 have >20)
Right reads:
Input : 21020
Mapped : 20499 (97.5% of input)
of these: 243 ( 1.2%) have multiple alignments (13 have >20)
97.5% overall read mapping rate.

Aligned pairs: 20463
of these: 237 ( 1.2%) have multiple alignments
216 ( 1.1%) are discordant alignments
96.3% concordant pair alignment rate.
Left reads:
Input : 9101
Mapped : 8598 (94.5% of input)
of these: 88 ( 1.0%) have multiple alignments (6 have >20)
Right reads:
Input : 9101
Mapped : 8597 (94.5% of input)
of these: 91 ( 1.1%) have multiple alignments (6 have >20)
94.5% overall read mapping rate.

Aligned pairs: 8583
of these: 88 ( 1.0%) have multiple alignments
86 ( 1.0%) are discordant alignments
93.4% concordant pair alignment rate.

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About Lisa Johnson

PhD candidate at UC Davis.
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