But when you are utilising python around almost every other listings, you will need to modify BS-Seeker2’s script very first

But when you are utilising python around almost every other listings, you will need to modify BS-Seeker2’s script very first

/.bashrc” (per-interactive-layer startup). Like, if the python highway is “/my_python/python”, excite change the first-line in “bs_seeker-generate.py”, “bs_seeker-line up.py” and “bs_seeker-call_methylation.py” to help you

Q: Easily have to only keep alignments one to map distinctively, is this a disagreement I ought to also provide right to Bowtie2 (through BS Seeker 2’s demand range alternative), or is that it an option that is available when you look at the BS Hunter dos by itself?

A: BS-Seeker2 records unique alignment automagically currently. If you wish to know how of numerous reads may have numerous attacks, work with BS-Seeker2 with parameter “–multiple-hit”.

Q: Just what must i carry out if for example the one or two friends possess overlaps? Ex: fragment size=150bp, one or two friends come in period of 100bp

Q: To have RRBS collection, the fresh new methylation quantities of C at 5′-CCGG-3′ internet are biased. Do BS-Seeker2 will bring mode for to avoid including bias?

A: Throughout the version v2.0.seven otherwise later on, BS-Seeker2 bring factor “–rm-CCGG” when you look at the “bs_seeker2-call-methylation.py”. To have RRBS collection, the newest orginal sequences might be slashed as gluey closes: 5′-CGGNNNN. NNNNC-3′ 3′-CNNNN. NNNNGGC-5′ Then artificial nucleotides is extra : 5′-CGGNNNN. NNNNCcg-3′ 3′-cgCNNNN. NNNNGGC-5′ Thus, the fresh new updates from fake cytosine may cause the prejudice. Brand new factor “–rm-CCGG” tend to get rid of the “5′-CCGG-3′” internet on the outputs.

A: Certain types of bowtie cannot work effectively for the BS-Seeker2. Even as we known, bowtie v1.2 linux can cause like problem, and you may latest types of bowtie might be ideal, for example bowtie v1.dos.step one.step one. I invited your declaration your circumstances so you can us, and we will enhance him or her here.

A: To own BS-Seeker2, it creates that declare for each and every chromosome/contig whenever strengthening the brand new list. Ergo if the genome include loads of scaffolds, after that there is excess files in a single folder on computer. And just have largely reduce the results having mapping the fresh BS-seq reads. Right here, we provide a couple apps for solving the fresh prolbem.

  • (first rung on the ladder): “ThreadFasta” : this option can assist you to threading 1000s of short scaffolds into high pseudo-chromosomes. As well, the application can establish “dictionary files” (stop which have “.dict) for transforming the position ranging from the fresh “pseudo-chromosome” and you may “brutal scaffolds”

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