[aniruddha.otago]

Hi Guys,

Recently we have published a paper in Nucleic Acids research on DNA methylation analysis- "Comparison of alignment software for genome-wide bisulphite sequence data". you might find it useful to have a look at it.. http://www.ncbi.nlm.nih.gov/pubmed/22344695

[sparks]

Hi,
I know this an old thread but I'd like to give an update on Novoalign bisulphite mode for those still interested.
Firstly Novoalign's algorithm is similar to BSMAP in that cytosines are retained in reads during alignment. The alignment works by converting Cs in the reference to CT dinucleotides just before alignment so a C or T in read will align with no penalty when aligned to a CT but Cs in read will mismatch a T in the reference. For negative strand alignments we do G to GA conversion.
In the next release V2.07.06 which should be out this week we've added a new program novomethyl that will call methylated cytosines from a SAM file. It's basically a samtools pileup with a SOAP SNP/Consensus calling algorithm that calls 6 nucelotide states (A, Cu, Cm, Gu, Gm, T ) rather than usual 4. Output is in form of a bed file.
To support this we also added a new tag in SAM format to indicate if read was aligned on Watson or Crick strand (i.e. in CT or GA mode)
If you'd like to try it we do give 1 month trial licences for free.
Colin
Novocraft Tech.

[zeam]

@lh3. I'm going to workshop over the next couple of days. It seems somebody else in my organisation has been using BSMAP with Arabidopsis bisulphite-Seq data. Below is their talk abstract. BSMAP would be particularly good for plant genomes considering all the CNG and CNN methylation. I'll see if I can get any slides.

"Hua Ying (CSIRO)
Approaches to mapping high-throughput bisulfite sequencing reads: High-throughput bisulfite sequencing is an attractive approach for analyzing genome-wide methylation patterns at a single-base-pair resolution. Although combining bisulfite conversion and high-throughput sequencing is increasingly widespread, its analysis is still problematic and limited to a few publications. A major challenge is the alignment of bisulfite-converted short reads to the reference genome due to increased search space and reduced sequence complexity as a result of the bisulfite conversion. Here, we took advantage of a recently published mapping algorithm BSMAP and demonstrated that BSMAP is more effective than previously used methods. By applying a two-step mapping strategy, we successfully mapped more than 90% of bisulfite short reads to the Arabidopsis genome."

Hi,there.You've mentioned "I'll see if I can get any slides.",and have you get the slides yet? If you have,Could you send a copy to me?I'm working on datas generated by BS_seq.THANKS!
Or could you give the e-mail adress of Hua Ying?My email:[email protected].

[fkrueger]

You've got mail.

Kind regards,
Felix

[aniruddha.otago]

Hi felix,

send you an email. Please reply.

[fkrueger]

Hi aniruddha.otago,

I am afraid I can't help you with interpreting the results from BSMAP, the output is probably described in the manual.

However I would like to point out that we have developed a BS-Seq mapping program called Bismark, which is easy to use, runs very fast and it performs methylation calling (in CpG, CHG and CHG context) in addition to just aligning the reads. Thus, its output is easy to handle and interpret and doesn't require you to start programming before you can have a look at the methylation data.

For more information please visit https://www.bioinformatics.bbsrc.ac....jects/bismark/ or search SEQanswers (and the SeqWiki) for Bismark.

In case you need any help just drop me an email.

Best wishes,
Felix

[ECO]

Hey. Welcome. Please don't constantly bump your thread. Give it some time and search the site for your answer.

[aniruddha.otago]

hi is there any feedback on my above query....

[aniruddha.otago]

I am copying a part of aligned read from BSMAP... Guys pease help how to interpret the methylation from here...... ur feedbacks will help me to have a clearer understanding of the data..




WI-EAS209_0006_FC706VJ:1:1:4692:4450#0/1 GGAGTGATTGTAGTTATGAATTTGATATGTTATTATTATTGTTGTTTGTGTTTTTTTTTTTTTTTTTGTTTTGATTTGGGAAGACAGTT NM
HWI-EAS209_0006_FC706VJ:1:1:4692:16063#0/1 GGAGTAAAAGGGTGAGAATTTATAGGAGGAATTTGTGGTCGATTAAATTTTTTTTTTTGGTTTTTTTTTGTTTTTGGGGGGGGGTTTAT NM
HWI-EAS209_0006_FC706VJ:1:1:4692:4011#0/1 GGGTTACGGAAAGTATATTTTTTGTTTTTTTGGTTTTGTTTGTTTTTGTGTAGTTTTAATAAGTATAGAGTAAGGAATATAATCGGTTT UM gi|29824588|ref|NC_000017.5|NC_000017 6309095 ++ 1 0:1:0:0:0 mC:6309101:6309178
HWI-EAS209_0006_FC706VJ:1:1:4693:4046#0/1 GGTAGGAGGATGGGGGGTTTTATATGGTTTTGTGTTATTTGTTTTATTTTTTTTTGTTTTTTGTGTGTTTTGTGGGGGAGGTTGGTTTT NM
HWI-EAS209_0006_FC706VJ:1:1:4693:10086#0/1 GGTTTTTTGGTTTTGTTATTCGTTAGTTTGGTTTGTTTTTGGTGATAGGGGGGGGGGGGCGTTTTTTTTTGTTTTTTTTTTTTTTTTTT NM
HWI-EAS209_0006_FC706VJ:1:1:4693:5806#0/1 GGAAGGTGTGGGTGGGTTGTTGATGGTGTTGTTTAGGGTATTTGGGGGTTTGAGATCGGAAGAGGGGTTCGGCGGGAATCCGGAGCCCG NM
HWI-EAS209_0006_FC706VJ:1:1:4693:6145#0/1 GGATGTTGGGTTGTTTTTGGGGGTGGGTGGTGATTTGTGGGGTTTGGGTTGTGTTTTTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTT NM
HWI-EAS209_0006_FC706VJ:1:1:4693:14513#0/1 GGATGATGTGTGGATTTTTGTGATTTTTGGGTTGGGATTTTTAATTGTTTGGGTTTTTTTGAGTTGGGAAGGGCGTTTCGGCGGGATTG NM
HWI-EAS209_0006_FC706VJ:1:1:4693:16592#0/1 ATTAAAGAGGTTAGGTATGGTGGTTTATGTTTGTAATTTTAGTATTTTGGGAGGTTGTGGGGGTGGTTTTTGGGGTTTTGGTTTTAGGT NM
HWI-EAS209_0006_FC706VJ:1:1:4693:2886#0/1 GGTTGGGGTAATTTAAAATTATATTTATTGGGTATATGTTTTTTTTTTTTTTTTATTTTGTTTTTTTTTTTGGTTGGTTTTTTTTTTGG NM
HWI-EAS209_0006_FC706VJ:1:1:4693:11171#0/1 GGGAATTTTGTTTTGTATTGTTGTGTATTTGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGACCTCGTATTCTGTCTTCTGT NM
HWI-EAS209_0006_FC706VJ:1:1:4693:11425#0/1 GGATTGCGGATTGTAGTGGCGTAATTTCGGTTTTTTGTAAGTTTCGTTTTTTGGGACCGGAAGGGCGGTTCGCGGGCATGCCGAGACCG NM
HWI-EAS209_0006_FC706VJ:1:1:4693:16325#0/1 GGAAGGTTTAGAATTTTTCGTATAATTGTGGGGTTAGGAGATTCGTAATATAGGTTTTTTTGGTTGCGTTGGGTGTCTGGGTGGTTGGT NM
HWI-EAS209_0006_FC706VJ:1:1:4693:18498#0/1 GGTAGTAGTTTTAGTGGTGTAGTTAGGTTATGGATATGTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTT NM
HWI-EAS209_0006_FC706VJ:1:1:4694:15719#0/1 GGTAATTATTGTTTGTTTTTTGGAGTTGTTGTTTGGGTAGGGGTGGTTTTGGTTTTTTTTTGTTTGGACGGGGAGGGGGGTTTGGGGGG NM
HWI-EAS209_0006_FC706VJ:1:1:4694:15747#0/1 GGATTGGTGTTTGTTTAGGTTATTGTTTTTGTGTTTGGTGTTGGTGGCGGGGTTGAGATGGGAAGGGGGGTTCCGCGGGACTGCGGAGC NM
HWI-EAS209_0006_FC706VJ:1:1:4694:20404#0/1 GGTTTTTTTTTTAAAAGTAGTTATGAGTAGATAAGTTTAGAAAGGGTTTTTTTTTCGTGTTTTTTTGGGGAAAATAGGGAAGGTTAATT NM
HWI-EAS209_0006_FC706VJ:1:1:4694:8674#0/1 GGTTGGGTTTTAGGTTGGAGTATGGTTGAGTTTTGTTTTTGTTTTTTTATTTGTTGGGGGGGGATTAAGTTATGTTTTTTTTTGTGGTT NM
HWI-EAS209_0006_FC706VJ:1:1:4694:19397#0/1 GGAGATTTTGGTTTTTTTAGGTTTTTTTTTGATTTAAATAAAAGTTGAGATCGGAAGAGCGGTTCAGCGGGAATGCCGAGCCCGTTTTG NM
HWI-EAS209_0006_FC706VJ:1:1:4694:17742#0/1 GGAATGGGTTGTGTTTTTTTGTTTTATTTGATTTAGTTAATGAATGTTGAGTATTTTTTTTGTTTAGGGTTTTGGGTTGGGAGGGGGGT NM
HWI-EAS209_0006_FC706VJ:1:1:4694:8920#0/1 GGGTTTAAGAGATTTTTTTGTTTTAGTTTTTTAAATAGTTGGGATTATAGGTATTTGTTTTTATGTTTGAGATCGGAAGAGCGGTTCAG NM
HWI-EAS209_0006_FC706VJ:1:1:4695:6571#0/1 GGGGGTTTTAGATTTGAATTAGGTTCGTCGGTTTTTTGTTGGTTGGGGGTTTTGTTTGGGTTTTTTTTTTTTTTTTTTTTTTTTGGTTT NM
HWI-EAS209_0006_FC706VJ:1:1:4695:5587#0/1 GGGAGTAGTTTTTTTTGTTTGTGTACGTTCGTATTTAGTAGATCGGAAGAGCGGTTCAGCAGAATGCCGAGACCGATCTCGTATCCCGT NM
HWI-EAS209_0006_FC706VJ:1:1:4695:8464#0/1 GGAATTTGTTTTTTAGCGGAGATAATGAGTTTTATTTATTTAGTTTAGGTAAGTGTCGGTCGTGGGTGGGGTATTTTGGTTTTTTTTTT UM gi|29824582|ref|NC_000011.4|NC_000011 3109475 -+ 4 0:0:0:0:1 mC:3109547:3109507:3109503
HWI-EAS209_0006_FC706VJ:1:1:4696:19770#0/1 GGGTATAGTGGTTTATATTTGTAATTTTAGTATTTTGGGAGGTTGAGGTAGGAAGATTATTTGAGTTTAGAAGAATAGTTCGGGTATTT UM gi|29824574|ref|NC_000003.5|NC_000003 45458886 -+ 2 0:0:1:0:0 mC

[aniruddha.otago]

I am copying a part of aligned read from BSMAP... Guys pease help how to interpret the methylation from here...... ur feedbacks will help me to have a clearer understanding of the data..

[aniruddha.otago]

did anybody used the BS_SEEKER programme ??? it seems that its faster than BSMAP. I tried to run BSMAP and it really slow. is that normal... anyfeedbacks from the previous users ??

[Zigster]

has anyone tried BSSeeker?

From what I can tell it is a Bowtie wrapper but not sure how it compares to the others discussed here.

[sci_guy]

hi sci_guy,
any news on this?

Not that I've heard of.

[volks]

Thanks! I'll take a look. I have more SOLiD data coming my way soon.

hi sci_guy,
any news on this? are there short read aligner other than SOCS2 capable of mapping BS reads in colorspace?
best, volks

[sci_guy]

I tried this in GSNAP (you have to pad everything to reach min lengths) and it chose ACGTTCA.

Cool. Thanks for that.

There's nothing like empirical data to disprove an hypothesis