Q: Each of my personal CGmap files features anywhere between step one,000 and you will dos,one hundred thousand ranking where new nucleotide is provided with instead of a motif, but rather merely “–” eg:
A: You might ask the fresh manager of your own group to put in pysam. If you don’t should bother your/her, you might need to build their python, after which arranged the brand new “pysam” plan. The following software could well be ideal for your.
A: So it error is linked that have pysam version. Evaluation playing with pysam v0.six.x do not have including error. Someone reports for example error while using pysam v0.seven.4. I have not sample most other pysam versions, and so are most happy if you you’ll inform us if it works on most other designs. Revision : When you look at the adaptation 2.1.2 and later, BS-Seeker2 consided the situation that have pysam type. For many who nonetheless deal with equivalent mistake even with you posting in order to 2.1.dos, you’re welcomed to send feedbacks to help you all of us.
Q: I attempted bs_seeker2-call_methylation.py, located brand new discover depth within the CGmap document is lower than 8000, where in fact the checks out can be a lot higher. (Thank-you Xuning Wang to possess figuring this issue and you may solve it)
A: It is associated from the that have parameter into the pileup form parsing in order to “pysam”. Regarding v2.step one.step three and later, alternative “-D” is added to own “bs_seeker2-call_methylation.py”. Member you will establish large amount of visibility limitation, in trade regarding costing additional time to own control.
A: If you find yourself with the “python” out of highway “/usr/bin/python”, you can physically range from the path regarding BS-Seeker2 into the file ” /.bash_profile” (bash) or ” /.profile” (almost every other shell) otherwise “
Q: Exactly what must i perform in case the a couple of friends provides overlaps?
/.bashrc” (per-interactive-shell business). But if you are utilising python around most other lists, you will need to change BS-Seeker2’s script first. Including, whether your python path try “/my_python/python”, please replace the first line when you look at the “bs_seeker-make.py”, “bs_seeker-fall into line.py” and you will “bs_seeker-call_methylation.py” to help you
Q: If i should simply remain alignments one to map uniquely, is it an argument I will likewise have straight to Bowtie2 (via BS Hunter 2’s demand range option), or perhaps is it an alternative that is available during the BS Seeker dos by itself?
A: BS-Seeker2 profile unique alignment automatically currently. If you would like recognize how of a lot reads possess several strikes, work with BS-Seeker2 that have factor “–multiple-hit”.
Q: Having RRBS library, the new methylation degrees of C from the 5′-CCGG-3′ benaughty PЕ™ihlГЎЕЎenГ sites try biased. Manage BS-Seeker2 brings setting getting to avoid such as prejudice?
A: Regarding the variation v2.0.seven or later on, BS-Seeker2 provide factor “–rm-CCGG” into the “bs_seeker2-call-methylation.py”. To own RRBS library, the fresh orginal sequences could well be slash as sticky closes: 5′-CGGNNNN. NNNNC-3′ 3′-CNNNN. NNNNGGC-5′ Upcoming phony nucleotides could be additional : 5′-CGGNNNN. NNNNCcg-3′ 3′-cgCNNNN. NNNNGGC-5′ Hence, the new condition regarding artificial cytosine will cause the fresh new prejudice. Brand new factor “–rm-CCGG” commonly beat most of the “5′-CCGG-3′” sites about outputs.
A: Specific sort of bowtie cannot work well for the BS-Seeker2. Once we understood, bowtie v1.2 linux can cause including problem, and you will newer types of bowtie will be ideal, like bowtie v1.2.1.step one. I acceptance you declaration your case to help you you, and we’ll revision her or him here.
A: To possess BS-Seeker2, it creates that apply for each chromosome/contig when building the new index. Thus in the event the genome consists of a lot of scaffolds, after that there is way too much records in a single folder on the computer. Right here, you can expect a couple of software to have fixing the new prolbem.
And possess mainly slow down the show to have mapping the BS-seq checks out
- (first rung on the ladder): “ThreadFasta” : this option can assist you to threading 1000s of quick scaffolds to the highest pseudo-chromosomes. On the other hand, the application will generate “dictionary data files” (avoid that have “.dict) to have changing the position ranging from the fresh “pseudo-chromosome” and you will “raw scaffolds”