What does it mean that: 100% of my alignment are discordant?

Question

[tiago211287]

Question: After the alignment with tophat, the summary shows:

Left reads:
          Input     :  12512968
           Mapped   :  12141005 (97.0% of input)
            of these:   2791920 (23.0%) have multiple alignments (81788 have >20)
Right reads:
          Input     :  12512968
           Mapped   :  12141005 (97.0% of input)
            of these:   2791920 (23.0%) have multiple alignments (81788 have >20)
97.0% overall read mapping rate.

Aligned pairs:  12141005
     of these:   2791920 (23.0%) have multiple alignments
                12140903 (100.0%) are discordant alignments

0.0% concordant pair alignment rate.

What does it mean? how can I fix this?

[tiago211287]

Thank you But I already fixed this issue. I think will run the files and merge the bam of the alignment instead of merging the fastq files before.

[datanerd]

Hi,

Please let me know how you solved it?

I merged - SORTMERNA then unmarked datafile Then trimmed using trimmomatic. Used the Paired output from trimmomatic for alignment. The alignment summary gives 100% discordant for all the samples. Please help!!!

Thanks! Mamta

Answer 1

[Pierre Lindenbaum]

Did you reverse-completed one file?

I would say: you mapped you reads using

aligner REF.fa R2.fq.gz R1.fq.gz

instead of

aligner REF.fa R1.fq.gz R2.fq.gz

[tiago211287]

I think I did that -.-

[Brian Bushnell]

That shouldn't cause a problem. The relative order of the R1 and R2 files does not matter. I think that perhaps he merged the reads in different orders, though, like this:

cat R1_L1.fq R1_L2.fq > R1.fq
cat R2_L2.fq R2_L1.fq > R2.fq

...or something along those lines.

[Pierre Lindenbaum]

ah yes, you're right. I thought I had this problem one day, I was wrong.