I think I did that -.-
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tiago211287
What does it mean that: 100% of my alignment are discordant?
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?
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Ram
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tiago211287
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tiago211287
1 answer
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
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Ram
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Pierre Lindenbaum
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Pierre Lindenbaum
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.
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Ram
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Brian Bushnell
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Brian Bushnell
ah yes, you're right. I thought I had this problem one day, I was wrong.
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Pierre Lindenbaum
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From what I knew, it means either the reads mapped are not in the correct orientation or the reads are not present in the correct insert size range.
Did again the same run using raw reads without
catmerge the fastq files and become this:What kind of library are you using - orientation, as @Prakki suggested, is the most likely problem.
What do you mean by "cat" the fastq?
merging different fastq files from different lanes from the illumina hiseq
I edited this
Okay, so did something go wrong during merging, do you know what caused the problem or are you still wondering? If so, what command did you use to merge the files?
If you paste your commands someone can point what went wrong.
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.
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