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Forum: Bioinformatics 06-28-2020, 12:19 PM
Replies: 0
Views: 619
Posted By metheuse
Imputation from targeted DNA sequencing?

We have done genotyping from targeted DNA sequencing of 600 related human samples. The targeted regions are mainly the exons of several hundred imprinted genes and the total size of the panel is 4Mb....
Forum: Bioinformatics 05-18-2017, 07:34 AM
Replies: 2
Views: 4,040
Posted By metheuse
Did you find the answer? I have the same question.

Did you find the answer? I have the same question.
Forum: Bioinformatics 07-17-2015, 12:46 PM
Replies: 9
Views: 11,985
Posted By metheuse
I'm also trying to measure...

I'm also trying to measure allele-specific-expression by exome-seq and RNA-seq, with the former to find heteroSNPs and alleles, and the latter to calculate ASE on the identified positions. I found...
Forum: Bioinformatics 06-19-2015, 10:29 AM
Replies: 0
Views: 1,070
Posted By metheuse
BWA properly paired reads are not really properly paired?

I selected properly paired (and mapq>=4) reads from BWA alignment by running:


Flagstat shows that this did remove most of the reads that have mates on different chr. However, several remain:

...
Forum: Bioinformatics 04-13-2015, 05:58 AM
Replies: 3
Views: 3,575
Posted By metheuse
Thanks! Your explanation makes sense. Then what...

Thanks! Your explanation makes sense.
Then what would be a good threshold for unique mapping in PE?
Forum: Bioinformatics 04-10-2015, 10:35 AM
Replies: 3
Views: 3,575
Posted By metheuse
BWA unique mapping

The question of how to get uniquely mapped reads from BWA-MEM really gives me a headache. I've searched online and found two ways:
1. Filter by mapq (different thresholds have been suggested: >=1,...
Forum: Epigenetics 03-26-2015, 11:10 AM
Replies: 0
Views: 1,639
Posted By metheuse
What control to use in RIP-seq?

I've seen people use IgG pull down, RIP-input or RNA-seq as controls in RIP-seq analysis. What is the difference between them? Thanks.
Forum: Bioinformatics 03-17-2015, 10:01 AM
Replies: 5
Views: 8,373
Posted By metheuse
Yes I read that and was wondering what...

Yes I read that and was wondering what "Repetitive hits will be randomly chosen." exactly means...
If it means choosing a random alignment when multiple locations are found to be equally best, then...
Forum: Bioinformatics 03-17-2015, 09:44 AM
Replies: 5
Views: 8,373
Posted By metheuse
Thanks, but I read that post before posting my...

Thanks, but I read that post before posting my questions.

There are controversial replies in that post. One reply says BWA makes random choice when there is a tie, but the last reply says: "if...
Forum: Bioinformatics 03-16-2015, 01:38 PM
Replies: 5
Views: 8,373
Posted By metheuse
How does BWA deal with multi mapping reads?

Bowtie manual clearly says the default mode is to report one alignment per read, and it will be random choice when tied.

BWA doesn't seem to be quite clear at this point in its manual. Can anyone...
Forum: Bioinformatics 08-06-2014, 12:10 PM
Replies: 2
Views: 2,564
Posted By metheuse
Hi, I got the same error saying "ERROR: Could not...

Hi, I got the same error saying "ERROR: Could not parse delta file, nucmer.data.delta error no: 400".
Did you find the solution? If yes, could you tell me? Thanks!
Forum: Epigenetics 02-11-2014, 12:09 PM
Replies: 6
Views: 3,413
Posted By metheuse
Thanks! I'll let you know if I have questions.

Thanks! I'll let you know if I have questions.
Forum: Epigenetics 02-11-2014, 10:43 AM
Replies: 6
Views: 3,413
Posted By metheuse
I have three replicates of MNase-seq of H3...

I have three replicates of MNase-seq of H3 sequencing reads, for two conditions of yeast. The aim is to find nucleosome positioning difference at some specific loci. Did you publish your tool...
Forum: De novo discovery 12-02-2013, 12:51 PM
Replies: 10
Views: 7,762
Posted By metheuse
Thanks a lot for all your replies above. I'm...

Thanks a lot for all your replies above. I'm currently trying velvetoptimizer and SGA on the data.

Besides, I have another question:
Do I have to choose the same Kmer size for error correction...
Forum: De novo discovery 11-28-2013, 09:41 AM
Replies: 10
Views: 7,762
Posted By metheuse
Thanks! It used 85% of the input reads, so still...

Thanks! It used 85% of the input reads, so still it can't explain the coverage difference.
Forum: De novo discovery 11-28-2013, 09:40 AM
Replies: 10
Views: 7,762
Posted By metheuse
Thanks! I'll take a look at Ray. I didn't try...

Thanks! I'll take a look at Ray.
I didn't try with random subsamples? Would that help?
Forum: De novo discovery 11-28-2013, 09:35 AM
Replies: 10
Views: 7,762
Posted By metheuse
Thanks a lot! I'll take a look at SGA and...

Thanks a lot! I'll take a look at SGA and velvetOptimizer.
Forum: De novo discovery 11-27-2013, 07:19 AM
Replies: 10
Views: 7,762
Posted By metheuse
Assembly with a single library always fail?

I'm trying to assemble a ~70M genome from a single Illumina PE library (100nt read, 160M each end, insert size=300bp).
I've tried velvet, Abyss, and SOAPdenovo with K=75. The largest N50 is 2kb,...
Forum: De novo discovery 11-22-2013, 03:01 PM
Replies: 4
Views: 3,601
Posted By metheuse
Thanks! I'll take a look.

Thanks! I'll take a look.
Forum: De novo discovery 11-21-2013, 09:45 AM
Replies: 4
Views: 3,601
Posted By metheuse
Thanks! But it seems that only when I submit...

Thanks! But it seems that only when I submit genomes to GenBank I can request annotation by this pipeline. Could I use this pipeline to analyze my data independent of submission?
Forum: De novo discovery 11-21-2013, 09:05 AM
Replies: 4
Views: 3,601
Posted By metheuse
Assembly annotation tool?

The purpose is to annotate de-novo bacteria genome assembly. I see there are many tools, like GeneMark, RAST, etc. Does any one have any recommendation, for de-novo annotation, and comparative...
Forum: Pacific Biosciences 11-20-2013, 07:06 AM
Replies: 9
Views: 4,122
Posted By metheuse
Thank you guys so much. I'll take a look into...

Thank you guys so much. I'll take a look into Cerulean.
Forum: Pacific Biosciences 11-19-2013, 01:30 PM
Replies: 9
Views: 4,122
Posted By metheuse
Thanks, Rhall! You've been always helpful to me! ...

Thanks, Rhall! You've been always helpful to me!
This should be a small genome. I'm not familiar with AHA. Is it something one can combine with the pacbioToCA-celera pipeline, or is it a parallel...
Forum: Pacific Biosciences 11-19-2013, 11:49 AM
Replies: 9
Views: 4,122
Posted By metheuse
Thanks. So my follow-up question is: is the...

Thanks. So my follow-up question is: is the pacbiotoca--> celera workflow a good way of "hybrid" assembly? Does it fully use the information from two technologies? As far as I know, this is the only...
Forum: Pacific Biosciences 11-19-2013, 09:27 AM
Replies: 9
Views: 4,122
Posted By metheuse
Hybrid assembling using PacBioToCA?

This may be a silly question. I know PacBioToCA can be used to correct PacBio long reads by alignment from, for example, Illumina short reads. Then the corrected PacBio reads can be assembled, for...
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