Similar protocols

Pipeline publication

[…] egions. When calculating the overlapping between QTL variants and motifs we considered all discovered motif instances within a binding region. For the QTL variants that do not overlap any motif variants, we used the motif instance within binding region with the best matching score as an anchor for calculating the distance., We also searched for other motifs at regions nearby (+−30 bp) the lead QTL variants as well as within the QTL binding regions. We extract sequences of the regions using software fastaFromBed of the BEDTools suite using reference sequence GRCh37. We then used software MEME to search for motifs. The discovered motifs were then compared against known motifs using software tomtom in JASPAR and UniPROBE databases. The discovered motifs are then provided to MSigDB for functional annotations., The most enriched motif was a CTCF related motif. After removing a number of low complexity motifs and cryptic repeats by manual inspection, the next most enriched motif was a G-rich motif similar to multiple SP-1 sites. There was not a strong accessory motif in these regions., With the peak profile identified above, we quantified the signal for each binding region by counting the number of sequencing fragments - read pairs. We applied stringent criteria by only counting the properly aligned read pairs with quality score at least 30 and excluding all the duplicated reads(samtools view -f 0x42 -F0x604 –q 30). We used Bedtools (v2.16.2) to count the intersection between fragments and identified binding regions. This produced an N by M matrix, where N is the number of samples and M is the number of binding regions. To evaluate the variation in the ChIP experiments, we compared the correlation between replicates grown on consecutive days and the correlation between all other samples. We found a mean pairwise correlation coefficient of 0.8314±0.0006 and 0.8202±0.0099 for the replicate sets for NA12891 and NA12892, respectively, while the mean pairwise correlation coefficient between samples was 0.1719±0.0177. This suggests a good signal noise ratio in the experiment., For the subsequent genetic analysis, we […]

Pipeline specifications

Software tools Tomtom, SAMtools, BEDTools