Q: Every one of my personal CGmap files features between step one,one hundred thousand and you will 2,100 ranks at which the fresh nucleotide is provided with as opposed to a motif, but instead simply “–” instance:
A: You can query the brand new officer of one’s people to install pysam. If not need certainly to bother him/the woman, you will need to build their python, right after which set-up brand new “pysam” bundle. Next script was helpful for you.
A: Which mistake is related which have pysam version. Review playing with pysam v0.6.x lack instance error. Some one profile such as mistake when using pysam v0.7.4. I have not attempt almost every other pysam designs, and so are really glad for people who you may inform us whether or not it works on most other products. Revision : In the variation 2.1.2 and later, BS-Seeker2 consided the challenge that have pysam variation. For folks who nevertheless face equivalent error even after your upgrade to help you dos.step 1.dos, you are welcomed to transmit feedbacks so you’re able to us.
Q: I tried bs_seeker2-call_methylation.py, discovered this new understand breadth in the CGmap file is definitely lower than 8000, in which the checks out are greater. (Thank you Xuning Wang to possess figuring this issue and you may solve it)
A: It’s associated by the having parameter from inside the pileup means parsing to “pysam”. Regarding the v2.step 1.3 and soon after, solution “-D” are extra having “bs_seeker2-call_methylation.py”. Associate you can expect to identify highest quantity of coverage limitation, in trade out of charging more hours to have operating.
A: When you are utilising the “python” away from road “/usr/bin/python”, you could potentially in person are the street regarding BS-Seeker2 in file ” /.bash_profile” (bash) or ” /.profile” (most other cover) otherwise “
Q: Exactly what should i would if your a couple friends keeps overlaps?
/.bashrc” (per-interactive-layer business). But when you are employing python under most other listings, you may want to change BS-Seeker2’s script earliest. Including, when your python path is actually “/my_python/python”, please change the first-line inside “bs_seeker-create.py”, “bs_seeker-fall into line.py” and “bs_seeker-call_methylation.py” to help you
Q: Basically must only continue alignments one to chart exclusively, is it a quarrel I should also have straight to Bowtie2 (through BS Hunter 2’s command range choice), or is this an alternative that’s available for the BS Hunter dos alone?
A: BS-Seeker2 accounts unique positioning automatically currently. If you’d like to know how of several checks out have numerous attacks, focus on BS-Seeker2 with parameter “–multiple-hit”.
Q: To have RRBS library, new methylation levels of C from the 5′-CCGG-3′ internet was biased. Carry out BS-Seeker2 will bring means having to avoid instance prejudice?
A: In the version v2.0.seven otherwise after, BS-Seeker2 render parameter “–rm-CCGG” within the “bs_seeker2-call-methylation.py”. To possess RRBS library, the latest orginal sequences might be clipped just like the sticky closes: 5′-CGGNNNN. NNNNC-3′ 3′-CNNNN. NNNNGGC-5′ Then fake nucleotides could well be extra : 5′-CGGNNNN. NNNNCcg-3′ 3′-cgCNNNN. NNNNGGC-5′ Ergo, the new standing of fake cytosine can cause the brand new bias. The fresh new factor “–rm-CCGG” tend to beat most of the “5′-CCGG-3′” web sites from the outputs.
A: Particular version of bowtie cannot work effectively during the BS-Seeker2. While we understood, bowtie v1 gay hookup apps like grindr.2 linux may cause instance situation, and new particular bowtie would-be suggested, particularly bowtie v1.2.1.step 1. I greeting your declaration your case so you can all of us, and we’ll posting them here.
A: To possess BS-Seeker2, it will make one to declare for each and every chromosome/contig whenever building the new index. Therefore if your genome include many scaffolds, after that there would be a lot of documents in a single folder with the computer. Right here, we provide two apps to have fixing the fresh new prolbem.
And possess mainly slow down the show having mapping brand new BS-seq reads
- (1st step): “ThreadFasta” : this choice can help you to threading a huge number of short scaffolds to the large pseudo-chromosomes. On the other hand, the application will generate “dictionary data” (prevent having “.dict) for converting the career anywhere between this new “pseudo-chromosome” and you will “intense scaffolds”