Q: Each of my CGmap files keeps ranging from 1,one hundred thousand and you will dos,100 ranks where brand new nucleotide is provided instead a motif, but alternatively merely «—» including:
A: You could potentially ask the brand new officer of the class to set up pysam. Otherwise need to irritate him/the woman, you may want to build the python, then build the fresh «pysam» package. The following software would-be great for you.
A: So it error is linked that have pysam adaptation. Analysis having fun with pysam v0.6.x lack for example error. Individuals profile for example error while using 
pysam v0.7.cuatro. We have not take to almost every other pysam types, and so are really happy for many who you will definitely inform us whether it deals with other versions. Change : During the version dos.step 1.dos and soon after, BS-Seeker2 consided the challenge having pysam variation. For people who still deal with similar mistake even with you improve so you can 2.step 1.dos, you are invited to send feedbacks so you’re able to all of us.
Q: I tried bs_seeker2-call_methylation.py, discover new comprehend breadth during the CGmap file is below 8000, where checks out might be a lot higher. (Thank-you Xuning Wang for figuring this issue and you may solve they)
A: It’s related by the which have parameter from inside the pileup form parsing to «pysam». Regarding v2.1.3 and later, alternative «-D» try additional getting «bs_seeker2-call_methylation.py». Member you will indicate large level of publicity restriction, as a swap away from costing more time getting operating.
A: When you’re by using the «python» off road «/usr/bin/python», you can actually range from the path away from BS-Seeker2 within the file » /.bash_profile» (bash) otherwise » /.profile» (most other layer) otherwise «
Q: Exactly what do i need to do when your a few mates has overlaps?
/.bashrc» (per-interactive-shell startup). But if you are using python around other lists, you may want to modify BS-Seeker2’s program basic. Like, in case your python street is actually «/my_python/python», delight change the first line inside «bs_seeker-generate.py», «bs_seeker-line-up.py» and «bs_seeker-call_methylation.py» so you’re able to
Q: Easily have to just remain alignments that chart distinctively, is it a disagreement I ought to also provide straight to Bowtie2 (through BS Hunter 2’s command range solution), or perhaps is so it an option that can be found from inside the BS Hunter dos by itself?
A: BS-Seeker2 records book alignment automatically already. If you’d like to know how of numerous reads could have numerous moves, focus on BS-Seeker2 having parameter «—multiple-hit».
Q: Having RRBS library, the newest methylation quantities of C on 5′-CCGG-3′ sites are biased. Manage BS-Seeker2 provides function to possess to prevent such bias?
A: On the version v2.0.7 otherwise afterwards, BS-Seeker2 offer parameter «—rm-CCGG» inside «bs_seeker2-call-methylation.py». For RRBS library, brand new orginal sequences might be cut because the sticky finishes: 5′-CGGNNNN. NNNNC-3′ 3′-CNNNN. NNNNGGC-5′ After that phony nucleotides could well be added : 5′-CGGNNNN. NNNNCcg-3′ 3′-cgCNNNN. NNNNGGC-5′ Therefore, new reputation regarding fake cytosine will cause the latest bias. The brand new parameter «—rm-CCGG» commonly eradicate all of the «5′-CCGG-3′» websites in the outputs.
A: Particular form of bowtie cannot work very well inside BS-Seeker2. While we recognized, bowtie v1.2 linux can cause eg state, and you can newer types of bowtie is suggested, eg bowtie v1.dos.1.step one. I allowed your report your own circumstances to us, and we will improve her or him here.
A: Having BS-Seeker2, it generates one to file for for each chromosome/contig whenever building the newest index. Hence if for example the genome include a number of scaffolds, next there is excessively data files in one single folder toward computer. Here, you can expect several software to possess solving the latest prolbem.
And get mainly slow down the results to have mapping the fresh BS-seq checks out
- (starting point): «ThreadFasta» : this program can help you to threading many brief scaffolds into the high pseudo-chromosomes. On the other hand, the applying will create «dictionary data files» (stop with «.dict) for transforming the career between the fresh new «pseudo-chromosome» and «raw scaffolds»