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Search: Posts Made By: shawpa
Forum: Epigenetics 02-19-2019, 10:22 AM
Replies: 1
Views: 3,173
Posted By shawpa
plotting BSSeq Data

I am interested to know what programs people use to plot CpG methylation data to create those pretty visuals you find in publications. I don't have any issues doing the analysis and identifying...
Forum: Bioinformatics 09-10-2018, 08:51 AM
Replies: 2
Views: 1,262
Posted By shawpa
If I use fixed windows versus number of CpG...

If I use fixed windows versus number of CpG windows as you are suggesting, is the concern that I will get no significance or that I will be flooded with regions of significance that are really false...
Forum: Bioinformatics 09-07-2018, 11:34 AM
Replies: 2
Views: 1,262
Posted By shawpa
Sliding window methylation analysis suggestions

I want to do sliding window analysis for differential methylation calculations for WGBS and target bisulfite sequencing libraries. Obviously I am not comparing the 2 library types against each other....
Forum: Bioinformatics 09-04-2018, 11:08 AM
Replies: 648
Views: 189,352
Posted By shawpa
divergent CpG dinucleotide methylation

I am not sure if this is the proper thread to post this on but since I am using bismark output, I thought I would ask here. I have very low coverage WGBS data. Ideally I would have higher coverage...
Forum: Bioinformatics 11-28-2017, 06:54 AM
Replies: 7
Views: 2,234
Posted By shawpa
Just for clarification... R2 singles need to be...

Just for clarification... R2 singles need to be aligned in pbat mode to get proper mapping?
Forum: Bioinformatics 11-28-2017, 05:22 AM
Replies: 7
Views: 2,234
Posted By shawpa
Thanks so much. That sounds like it will work.

Thanks so much. That sounds like it will work.
Forum: Bioinformatics 11-27-2017, 07:51 AM
Replies: 7
Views: 2,234
Posted By shawpa
when to merge PE and SE alignments in Bismark

Due to some R2 quality issues (I think), I am getting low paired end mapping efficiencies. When I align the unmapped reads in single end mode, I am able to recover quite a few of the reads. I am...
Forum: Bioinformatics 09-14-2017, 11:25 AM
Replies: 0
Views: 1,165
Posted By shawpa
allele balance filtering

I am looking for some advice on hard filtering by allele balance.

I have 94 exomes that have been analyzed using the GATK pipeline per the current “Best Practices”. I did VQSR and filtered for...
Forum: Bioinformatics 09-14-2017, 11:05 AM
Replies: 0
Views: 743
Posted By shawpa
hard filtering with allele balance

I am looking for some advice on hard filtering based on allele balance (either over the entire cohort or by sample).

Sorry this post my be long but I wanted to give a little background. I have 94...
Forum: Bioinformatics 11-30-2016, 05:51 AM
Replies: 18
Views: 5,394
Posted By shawpa
I realize this is an outdated thread but I am...

I realize this is an outdated thread but I am trying to run CONIFER for the first time and having some issues. I cannot run the very first command to generate the RPKM files. Like someone said above,...
Forum: Metagenomics 03-18-2016, 09:13 AM
Replies: 0
Views: 1,278
Posted By shawpa
modify megan5 taxonomy paths output

I was using the "path" export option in megan5 to output the full taxonomy of some bacterial sequencing reads. The issue that I am having with this export option is that the number of fields is not...
Forum: Bioinformatics 02-17-2016, 08:13 AM
Replies: 2
Views: 796
Posted By shawpa
Oh thank you. I have been going crazy trying to...

Oh thank you. I have been going crazy trying to figure this out.
Forum: Bioinformatics 02-17-2016, 08:08 AM
Replies: 2
Views: 796
Posted By shawpa
bowtie output not suppressing reads

I am doing single end alignment with bowtie. I don't want any mismatches and I only want to keep reads that mapped uniquely. I used the options -v 0 and -m 1. The issue I am having is that it seems...
Forum: Bioinformatics 12-17-2014, 05:14 AM
Replies: 1
Views: 1,011
Posted By shawpa
test for randomness of sequencing reads or enrichment

I have a very large sequencing library and I am looking for a way to test whether the DNA that I sequenced represents the entire genome or whether there is some enrichment of regions. I don't mean...
Forum: Bioinformatics 07-28-2014, 10:17 AM
Replies: 138
Views: 48,162
Posted By shawpa
I have used trim galore before using Bismark many...

I have used trim galore before using Bismark many times. It just occurred to me though that there might be a problem in my use of the pipeline. What I usually do is trim the reads (both adaptor and...
Forum: Bioinformatics 08-05-2013, 06:51 AM
Replies: 27
Views: 13,505
Posted By shawpa
I actually did try that, but I couldn't get the...

I actually did try that, but I couldn't get the bismark2bedgraph command to read any input files. I used the following command executed from the folder containing my methylation extractor output...
Forum: Bioinformatics 08-05-2013, 06:16 AM
Replies: 27
Views: 13,505
Posted By shawpa
bedgraph for CHH and CHG methylation only

I am trying to generate separate bedgraph files for CHH and CHG methylation contexts like in the previous post. Th only options available in bismark seem to be CpG or All contexts when it comes to...
Forum: Bioinformatics 08-21-2012, 05:55 AM
Replies: 648
Views: 189,352
Posted By shawpa
temp directory for bismarktobedgraph script

I am using the bismarktobedgraph script from the website. Because it doesn't have a temp directory option I am running it from the directory that has the space. It seems that it is running out of...
Forum: Bioinformatics 08-20-2012, 06:52 AM
Replies: 0
Views: 3,119
Posted By shawpa
picard error: Mismatch between read length and quals length writing read

I am getting an error in picard when trying to merge some sam files. I can't find this error posted about anywhere. I am wondering if someone knows what it might mean and how i can go about fixing...
Forum: Illumina/Solexa 08-15-2012, 07:27 AM
Replies: 10
Views: 5,277
Posted By shawpa
I heard that illumina is coming out with a QC kit...

I heard that illumina is coming out with a QC kit for titrating libraries on the MiSeq. I guess they are listening to all the complaints about clustering concentrations and wasting runs. Don't know...
Forum: Bioinformatics 08-14-2012, 07:32 AM
Replies: 189
Views: 75,243
Posted By shawpa
Please disregard. I was being stupid. My values...

Please disregard. I was being stupid. My values are in phred33.
Forum: Bioinformatics 08-14-2012, 07:26 AM
Replies: 189
Views: 75,243
Posted By shawpa
quality values for trimmomatic

I am having trouble understanding the quality value used in trimmomatic. I want to trim bases from 3' and 5' ends that are below Q20. I have Illumina 1.8+ so my quality values are phred64. For the...
Forum: Bioinformatics 08-13-2012, 06:40 AM
Replies: 648
Views: 189,352
Posted By shawpa
error with Prinseq output file to bismark?

I was wondering if anyone has used prinseq to trim fastq files then tried to put those fastq files into bismark for alignment and had any issues. I generated some trimmed fastq files and when I try...
Forum: Illumina/Solexa 07-27-2012, 04:39 AM
Replies: 75
Views: 33,611
Posted By shawpa
I can't give you any further advice on the phiX....

I can't give you any further advice on the phiX. If what you are doing works and you get good clustering from it, then I would keep doing what you are doing. All I can say is that we use the kit. I...
Forum: Illumina/Solexa 07-25-2012, 03:26 AM
Replies: 75
Views: 33,611
Posted By shawpa
I don't know what the "standards" are in the kapa...

I don't know what the "standards" are in the kapa library quantification kit. If you say they are phiX then they probably are. However, they are already diluted and you just pipette them into the...
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