Q: Every one of my CGmap documents have between step 1,100 and you can 2,one hundred thousand positions of which the latest nucleotide is offered instead a motif, but alternatively merely “–” including:
A: You can ask this new officer of your own cluster to set up pysam. Otherwise need to irritate him/the lady, you may want to create your python, and then install new “pysam” plan. https://datingmentor.org/tr/bbw-tarihleme/ Another program is helpful for you.
A: So it mistake is related with pysam variation. Evaluation using pysam v0.six.x lack such as for instance mistake. Someone reports such mistake while using the pysam v0.seven.4. I haven’t decide to try most other pysam brands, and are usually really grateful if you you are going to let us know whether or not it deals with almost every other models. Upgrade : Inside version 2.1.2 and soon after, BS-Seeker2 consided the problem which have pysam type. For those who nevertheless face similar error even with you revise so you can dos.1.2, you’re asked to send feedbacks to united states.
Q: I tried bs_seeker2-call_methylation.py, discover the latest understand breadth in the CGmap document is definitely below 8000, where in actuality the checks out might be greater. (Many thanks Xuning Wang for figuring this issue and you can resolve it)
A: It is related from the having parameter during the pileup setting parsing to “pysam”. On v2.1.step three and soon after, choice “-D” try additional having “bs_seeker2-call_methylation.py”. Affiliate could establish highest amount of publicity limitation, in exchange off costing longer getting control.
A: If you are by using the “python” away from path “/usr/bin/python”, you might privately range from the highway off BS-Seeker2 into the document ” /.bash_profile” (bash) or ” /.profile” (other layer) otherwise “
Q: What ought i carry out if the one or two mates possess overlaps?
/.bashrc” (per-interactive-shell startup). But when you are utilizing python not as much as almost every other listings, you will need to modify BS-Seeker2’s program earliest. Such as for instance, in the event your python street is actually “/my_python/python”, please replace the first line for the “bs_seeker-create.py”, “bs_seeker-line up.py” and you can “bs_seeker-call_methylation.py” to
Q: Basically should only keep alignments you to definitely chart distinctively, so is this an argument I should likewise have right to Bowtie2 (via BS Seeker 2’s demand range option), or perhaps is it a choice which can be found from inside the BS Hunter 2 by itself?
A: BS-Seeker2 account book positioning by default already. If you would like know the way of many reads have numerous moves, work with BS-Seeker2 having factor “–multiple-hit”.
Q: Having RRBS collection, the fresh methylation degrees of C at the 5′-CCGG-3′ web sites is biased. Perform BS-Seeker2 brings function to possess to avoid such as for example bias?
A: Regarding the variation v2.0.7 otherwise after, BS-Seeker2 offer parameter “–rm-CCGG” in “bs_seeker2-call-methylation.py”. For RRBS library, this new orginal sequences would-be clipped as the gluey comes to an end: 5′-CGGNNNN. NNNNC-3′ 3′-CNNNN. NNNNGGC-5′ After that phony nucleotides is additional : 5′-CGGNNNN. NNNNCcg-3′ 3′-cgCNNNN. NNNNGGC-5′ For this reason, the brand new reputation from artificial cytosine can cause the latest prejudice. The fresh new factor “–rm-CCGG” commonly beat most of the “5′-CCGG-3′” web sites regarding outputs.
A: Specific variety of bowtie does not work for the BS-Seeker2. Once we known, bowtie v1.dos linux will cause such as condition, and you may new types of bowtie might be suggested, such as for example bowtie v1.dos.step 1.1. I anticipate you report their circumstances so you’re able to us, and we’ll revise them here.
A: To possess BS-Seeker2, it will make one to file for for every single chromosome/contig whenever strengthening the brand new list. Ergo in case your genome includes numerous scaffolds, then there would be way too much data files in a single folder on computer. Right here, we provide a couple apps to have solving this new prolbem.
And then have mostly reduce the results getting mapping the newest BS-seq checks out
- (first step): “ThreadFasta” : this choice can help you to threading a great deal of quick scaffolds on high pseudo-chromosomes. At the same time, the applying can establish “dictionary data files” (stop that have “.dict) to own changing the positioning between the fresh new “pseudo-chromosome” and you will “brutal scaffolds”