Dear all hi,
I have paired end chip-exo data. The interesting is, both reads from each of the pair was already mapped and peaks were called. I have data in BED format which caused a confusion because of the paired end reads. Even though I have found couple softwares for paired chip-exo analysis, they all require bam input. I dont want to do all the alignment again therefore I wanted ask the community of booster.
My aim is to get BigWig file format for visualisation and ~250 bp peaks for the data process(finding overlaps etc.);
1) I am totally lost for the bigwig part so I beg for your information. Can I obtain BigWig with current available information? (I checked bed to BigWig threads from seq answers and biostars but can I solve it with using bedtools genomeconv)
2) For obtaining ~250 bp peaks I thought merging them with bedtools could be a solution. Is there a gold standard for merging process ?
Could you enlighten me a bit. Any document regarding this information would be very useful as well.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43785 — > source of the data.
Tuncs-MacBook-Pro:~ morova$ more /Volumes/blackhole/chip-exo/GSE43785_RAW/GSM1071284_120424_ChipEXO5_NoIndex_L005_R1.fastq.tagAlign.bed chr12 79171842 79171891 - chr4 144341449 144341498 - chr3 42101448 42101497 - chr19 18496785 18496834 + chr3 24961259 24961308 + chr5 4818754 4818803 + chr10 88177242 88177291 + chr2 45031538 45031587 + chr3 190478599 190478648 + chr20 8807491 8807540 -
Thank you for your help,