Question: What does it mean that: 100% of my alignment are discordant?
0
gravatar for tiago211287
4.2 years ago by
tiago2112871.1k
USA
tiago2112871.1k wrote:

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?

rna-seq alignment tophat • 1.8k views
ADD COMMENTlink modified 4.2 years ago by Pierre Lindenbaum123k • written 4.2 years ago by tiago2112871.1k

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.

ADD REPLYlink written 4.2 years ago by tiago2112871.1k

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

ADD REPLYlink written 3.6 years ago by Mamta440
1
gravatar for Pierre Lindenbaum
4.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

 

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
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Pierre Lindenbaum123k
1

I think I did that -.-

ADD REPLYlink written 4.2 years ago by tiago2112871.1k
1

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.

ADD REPLYlink written 4.2 years ago by Brian Bushnell16k

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

ADD REPLYlink written 4.2 years ago by Pierre Lindenbaum123k
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