Question: Chip-seq mapping (using bowtie2 & tophat2) What's different ?
gravatar for leenaehyeon
3.5 years ago by
Korea, Republic Of
leenaehyeon10 wrote:

I mapped my sample (Chip-seq) using bowtie2 & tophat2 to find out about the difference.

1. boetie2 -x mm10 -1 sample1.fastq -2 sample2.fastq -S sample_mapped.sam


12729154 reads; of these:

12729154 (100.00%) were paired; of these:

2525573 (19.84%) aligned concordantly 0 times

7713508 (60.60%) aligned concordantly exactly 1 time

2490073 (19.56%) aligned concordantly >1 times


2525573 pairs aligned concordantly 0 times; of these:

777420 (30.78%) aligned discordantly 1 time


1748153 pairs aligned 0 times concordantly or discordantly; of these:

3496306 mates make up the pairs; of these:

1563238 (44.71%) aligned 0 times

1052885 (30.11%) aligned exactly 1 time

880183 (25.17%) aligned >1 times

93.86% overall alignment rate

                     ------------> I understand mapping rate is 93.86%


2. tophat2 -o tophat_out_sample -G mm10.gtf --transcriptome-index mm10_transcripts --library-type fr-firststrand mm10 sample1_fastq sample2_fastq


Left reads:

Input : 12729154

Mapped : 10520541 (82.6% of input)

of these: 1021764 ( 9.7%) have multiple alignments (206443 have >20)

Right reads:

Input : 12729154

Mapped : 9983465 (78.4% of input)

of these: 949034 ( 9.5%) have multiple alignments (206223 have >20)

80.5% overall read mapping rate.


Aligned pairs: 9223914

of these: 837455 ( 9.1%) have multiple alignments

586051 ( 6.4%) are discordant alignments

67.9% concordant pair alignment rate.

     --------------------->I understand mapping rate is 67.9%


If I was wrong, Each outcome is what does mean?

and Why tophat2 & bowtie2 has different outcome? :(  I heard that bowtie2 is more normally used for ChIP-seq.


chip-seq • 2.3k views
ADD COMMENTlink modified 3.5 years ago by h.mon24k • written 3.5 years ago by leenaehyeon10

tophat is useful when you expect to have large gaps in the alignment of your reads to the reference, which is the common situation if the read is coming from cDNA and could therefore bridge an intron. 

ADD REPLYlink written 3.5 years ago by Martombo2.4k
gravatar for h.mon
3.5 years ago by
h.mon24k wrote:

For ChIP-seq, you should map your reads against the genome, so bowtie is an appropriate tool.

Tophat is a splice junction mapper for RNA-Seq reads. From your command line, you are mapping against mouse transcriptome, your mapping rate will be lower than the bowtie mapping because you are sequencing across the genome and mapping on transcriptome only.

ADD COMMENTlink written 3.5 years ago by h.mon24k

Really happy to your reply. Thank you!!!!

I'll try bowtie2 mapping for Chip-seq! :))))

ADD REPLYlink written 3.5 years ago by leenaehyeon10
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