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Forum: Bioinformatics 05-24-2016, 07:45 AM
Replies: 136
Views: 41,314
Posted By crazyhottommy
Thanks, I noticed that as well and change the...

Thanks, I noticed that as well and change the length accordingly.

We are checking the bisulfite conversion rate.
Although in the human genome, non-CpGs are unmethylated, if there is a bisulfite...
Forum: Bioinformatics 05-24-2016, 06:57 AM
Replies: 136
Views: 41,314
Posted By crazyhottommy
check 4 cases?

Thanks for the script.
what I thought:

I will need to check CCG + adaptor or TCG + adaptor for unmethylated filled-in Cs.
and CTG + adaptor or TTG + adaptor for methylated filled-in Cs.

e.g....
Forum: Bioinformatics 05-23-2016, 12:19 PM
Replies: 136
Views: 41,314
Posted By crazyhottommy
That would be very helpful! Thanks!

That would be very helpful!
Thanks!
Forum: Bioinformatics 05-23-2016, 09:15 AM
Replies: 136
Views: 41,314
Posted By crazyhottommy
most of my samples have a spike-in lambda...

most of my samples have a spike-in lambda unmethylated DNA. I mapped them to lambda genome and calculated the efficiency. I do not have spike-in for one sample. I have to check the conversion...
Forum: Bioinformatics 01-24-2016, 04:20 PM
Replies: 6
Views: 1,953
Posted By crazyhottommy
Thanks, I would like to read the manuscript....

Thanks, I would like to read the manuscript. Please send to tangming2005@gmail.com

I will be testing bam-matcher in the near future, and I will come back to you when I have questions.

Thanks...
Forum: Bioinformatics 01-23-2016, 06:46 PM
Replies: 6
Views: 1,953
Posted By crazyhottommy
Thanks Paul for your answer. For ChIP-seq, I...

Thanks Paul for your answer.
For ChIP-seq, I can call peaks and find the regions with enough depth, DP >15 as suggested in bitbucket page.

I can also find regions with enough reads for WES. So, I...
Forum: Bioinformatics 01-23-2016, 06:23 PM
Replies: 6
Views: 1,953
Posted By crazyhottommy
I have bam files for Whole exome sequencing(100...

I have bam files for Whole exome sequencing(100 bp paired-end) and ChIP-seq (36bp single end) from the same sample, can I still use the tool?
ChIP-seq only has signals where the protein or histone...
Forum: Bioinformatics 04-17-2015, 06:55 AM
Replies: 7
Views: 2,658
Posted By crazyhottommy
Thanks, I updated the post accordingly.

Thanks, I updated the post accordingly.
Forum: Bioinformatics 04-15-2015, 08:19 AM
Replies: 7
Views: 2,658
Posted By crazyhottommy
see my post here...

see my post here http://crazyhottommy.blogspot.com/2013/06/convert-eland-sortedtxt-to-bam-file.html
Forum: Bioinformatics 11-24-2014, 09:45 AM
Replies: 6
Views: 15,480
Posted By crazyhottommy
Just try to plot the heatmap, do not assign it to...

Just try to plot the heatmap, do not assign it to hm. Do you see a heatmap?
Forum: Bioinformatics 11-19-2014, 10:07 AM
Replies: 18
Views: 5,301
Posted By crazyhottommy
for trimming phred scores, trim at 5 not 20. ...

for trimming phred scores, trim at 5 not 20.
see here http://genomebio.org/nail-in-the-quality-trimming-coffin/
and paper here :
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3908319/
Forum: Bioinformatics 11-10-2014, 06:28 AM
Replies: 1
Views: 1,030
Posted By crazyhottommy
I had some experience with diffreps...

I had some experience with diffreps https://code.google.com/p/diffreps/
other tools http://omictools.com/medip-seq-c350-p1.html

see my posts:...
Forum: Bioinformatics 10-22-2014, 10:49 AM
Replies: 2
Views: 1,510
Posted By crazyhottommy
try Rcount...

try Rcount http://bioinformatics.oxfordjournals.org/content/early/2014/10/15/bioinformatics.btu680.abstract
Forum: Bioinformatics 09-03-2014, 09:08 AM
Replies: 3
Views: 6,102
Posted By crazyhottommy
see here Paper: RPKM measure is inconsistent...

see here Paper: RPKM measure is inconsistent among samples http://www.ncbi.nlm.nih.gov/pubmed/?term=22872506
and here http://blog.nextgenetics.net/?e=51
Forum: Bioinformatics 08-22-2014, 05:25 AM
Replies: 14
Views: 4,614
Posted By crazyhottommy
you should get rid of the last five lines: ...

you should get rid of the last five lines:

Just use this single command to merge the HTSeq count results:
paste *txt | cut -f1,2,4,6,8,10,12,14,16,18,20,22,24,26 | head -n -5 > counts.txt
Note:...
Forum: Bioinformatics 08-20-2014, 10:16 AM
Replies: 14
Views: 4,614
Posted By crazyhottommy
Have a look at my post...

Have a look at my post http://crazyhottommy.blogspot.com/2013/10/rna-seq-analysis-samtools-sort-and.html
Forum: Bioinformatics 08-04-2014, 06:48 PM
Replies: 4
Views: 1,373
Posted By crazyhottommy
I merged the sequences reads for ChIP-seq, and it...

I merged the sequences reads for ChIP-seq, and it is fine. I am not sure with RNA-seq
Forum: Bioinformatics 08-04-2014, 06:48 PM
Replies: 4
Views: 1,373
Posted By crazyhottommy
I also want to know some insights in this issue.

I also want to know some insights in this issue.
Forum: Bioinformatics 07-31-2014, 11:09 AM
Replies: 6
Views: 9,420
Posted By crazyhottommy
it is an old post, I have an old post addressing...

it is an old post, I have an old post addressing this http://crazyhottommy.blogspot.com/2013/04/batch-converting-coordinates-to.html
Forum: Bioinformatics 07-31-2014, 07:50 AM
Replies: 14
Views: 2,393
Posted By crazyhottommy
see my updated code. you need to add "\n" at the...

see my updated code. you need to add "\n" at the last line of the code.
https://gist.github.com/crazyhottommy/a59df92b48e6ad3f4630
Forum: Bioinformatics 07-30-2014, 12:17 PM
Replies: 3
Views: 1,314
Posted By crazyhottommy
No replicates is a bad experimental design. ...

No replicates is a bad experimental design.
Next maSigPro: updating maSigPro Bioconductor
package for RNA-seq time series

and here http://www.hindawi.com/journals/bmri/2013/203681/
Forum: Bioinformatics 07-27-2014, 04:37 PM
Replies: 4
Views: 1,261
Posted By crazyhottommy
http://www.nature.com/nprot/journal/v8/n9/full/npr...

http://www.nature.com/nprot/journal/v8/n9/full/nprot.2013.099.html

and

http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
Forum: Bioinformatics 07-22-2014, 01:42 PM
Replies: 14
Views: 2,393
Posted By crazyhottommy
I see, just changed the second last line code to:...

I see, just changed the second last line code to:

ofile.write(line + "\n")

let me know if it works or not.

https://gist.github.com/crazyhottommy/a59df92b48e6ad3f4630
Forum: Bioinformatics 07-22-2014, 11:23 AM
Replies: 14
Views: 2,393
Posted By crazyhottommy
I am sorry, the awk does not work in this case,...

I am sorry, the awk does not work in this case, awk use $1 for first word and $2 for the second word.

I just wrote a python script below, and I tested it, it worked fine.
myfasta file
...
Forum: Bioinformatics 07-22-2014, 10:15 AM
Replies: 14
Views: 2,393
Posted By crazyhottommy
you may use awk: ...

you may use awk:
http://stackoverflow.com/questions/11678939/replace-text-based-on-a-dictionary

Usage: awk -f foo.awk dict.dat user.dat...
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