Q: All of my CGmap data has between step 1,000 and you will dos,one hundred thousand ranks of which new nucleotide is provided with in place of a theme, but alternatively only “–” particularly:

A: You could potentially ask this new manager of your own party to install pysam. Otherwise have to irritate him/the lady, you might need to build the python, and build the newest “pysam” plan. Another program was helpful for your.

A: That it error is linked which have pysam adaptation. Testing playing with pysam v0.6.x would not have such as error. Someone account like mistake when using pysam v0.7.4. We haven’t attempt most other pysam brands, and are also very grateful for people who you may let us know when it deals with other systems. Change : During the adaptation dos.step one.dos and soon after, BS-Seeker2 consided the difficulty having pysam version. For folks who nevertheless deal with equivalent error despite you posting to 2.step one.2, you are invited to deliver feedbacks to help you us.

Q: I attempted bs_seeker2-call_methylation.py, discovered the fresh realize breadth when you look at the CGmap file is below 8000, in which the reads should be higher. (Thank-you Xuning Wang to own figuring this issue and you can resolve it)

A: It is associated by having parameter for the pileup setting parsing to “pysam”. From the v2.step one.step three and soon after, option “-D” is extra to have “bs_seeker2-call_methylation.py”. Representative could identify highest number of visibility limitation, as a swap out-of costing more hours getting processing.

A: If you are making use of the “python” out-of road “/usr/bin/python”, you could privately range from the roadway of BS-Seeker2 into the document ” /.bash_profile” (bash) or ” /.profile” (almost every other layer) or “

Q: Just what can i carry out in case your several mates has actually overlaps?

/.bashrc” (per-interactive-shell business). But if you are utilising python not as much as most other listing, you may want to modify BS-Seeker2’s software earliest. For example, if the python roadway try “/my_python/python”, please change the first-line in “bs_seeker-create.py”, “bs_seeker-make.py” and you can “bs_seeker-call_methylation.py” so you’re able to

Q: Basically must merely remain alignments one to map uniquely, so is this an argument I ought to also provide straight to Bowtie2 (via BS Seeker 2’s command range alternative), or perhaps is which an option that is available from inside the BS Hunter dos alone?

A: BS-Seeker2 records novel positioning automatically already. If you wish to understand how of numerous checks out might have multiple strikes, work on BS-Seeker2 having factor “–multiple-hit”.

Q: For RRBS collection, the fresh new methylation degrees of C on 5′-CCGG-3′ websites is biased. Do BS-Seeker2 will bring means to possess to avoid for example bias?

A: On variation v2.0.seven or later on, BS-Seeker2 render parameter “–rm-CCGG” for the “bs_seeker2-call-methylation.py”. To have RRBS collection, the fresh new orginal sequences will be slashed as sticky ends up: 5′-CGGNNNN. NNNNC-3′ 3′-CNNNN. NNNNGGC-5′ Up coming fake nucleotides might be added : 5′-CGGNNNN. NNNNCcg-3′ 3′-cgCNNNN. NNNNGGC-5′ Hence, the brand new condition out-of phony cytosine will cause the brand new bias. This new factor “–rm-CCGG” will reduce most of the “5′-CCGG-3′” web sites about outputs.

A: Bu Web sitesine bak Certain type of bowtie does not work during the BS-Seeker2. Once we identified, bowtie v1.2 linux can cause such problem, and you can brand new sorts of bowtie will be suggested, such bowtie v1.2.step 1.1. We invited you declaration your case to you, and we will change them here.

A: Having BS-Seeker2, it creates one to apply for for each and every chromosome/contig when building the list. Therefore in the event the genome include enough scaffolds, next there is too much documents in a single folder toward computer. Right here, you can expect a few programs getting fixing new prolbem.

And possess mainly reduce the overall performance getting mapping the fresh new BS-seq reads

• (starting point): “ThreadFasta” : this program can help you to threading a huge number of small scaffolds toward higher pseudo-chromosomes. While doing so, the applying will create “dictionary documents” (end having “.dict) getting changing the positioning between the newest “pseudo-chromosome” and you can “intense scaffolds”