Hi I was trying to play with some published ChIP-seq data. I noticed that the aligned reads presented has extremely sharp peaks (attached figure A), so I cooked the original data to see whether I could get similar results.
bowtie2 -p 15 -x ~/Bowtie2Index/genome -U SRR561494.fastq.gz -S TregFoxp3ChIP_by_Rudensky.sam >& out.txt & samtools view -bS TregFoxp3ChIP_by_Rudensky.sam > TregFoxp3ChIP_by_Rudensky.bam & samtools sort TregFoxp3ChIP_by_Rudensky.bam -o TregFoxp3ChIP_by_Rudensky.sorted.bam & samtools index TregFoxp3ChIP_by_Rudensky.sorted.bam TregFoxp3ChIP_by_Rudensky.sorted.bai &
convert the bam file into bw file using bamTobw.sh enter link description here and load the bw file on to the IGV browser.
but somehow I could not get sharp peaks like the published figure as shown here. Is the author use some specific method to visualize the mapped reads, or something wrong with my cooking of the data? if any idea, please let me know. Tsk!