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Search: Posts Made By: woodydon
Forum: Bioinformatics 03-31-2015, 01:35 AM
Replies: 6
Views: 1,060
Posted By woodydon
Hi Brian and elkjournals1, I found the...

Hi Brian and elkjournals1,

I found the solution for this after consulting with a GATK developer. Please refer to this post:
...
Forum: Bioinformatics 03-30-2015, 01:13 AM
Replies: 6
Views: 1,060
Posted By woodydon
Hi Brain, I am sorry that I misunderstood...

Hi Brain,

I am sorry that I misunderstood your response. I will map them separately and merge the bam files for the following GATK steps. I will report if I succeed.

Thanks,
Woody
Forum: Bioinformatics 03-30-2015, 01:04 AM
Replies: 6
Views: 1,060
Posted By woodydon
Hi Brian, Thanks for the response! I...

Hi Brian,

Thanks for the response!

I combined the fastq files and ran BWA-MEM to generate a bam file. I used GATK's RealignerTargetCreator to create target regions for IndelRealigner. But,...
Forum: Bioinformatics 03-29-2015, 11:33 PM
Replies: 6
Views: 1,060
Posted By woodydon
Smile Working with input files with Q64 and Q33 (GATK IndelRealigner)

Dear SEQanswers members,

I have two input fasta files from exome-seq. One is coded with Q64 and the other is coded with Q33 quality scores. I want to combine the two input fasta files and run...
Forum: Illumina/Solexa 09-14-2014, 11:29 PM
Replies: 13
Views: 3,236
Posted By woodydon
How was the quality of 2x250 bp reads? 25 million...

How was the quality of 2x250 bp reads? 25 million read pairs per run?

Woody
Forum: Illumina/Solexa 09-14-2014, 11:28 PM
Replies: 25
Views: 2,804
Posted By woodydon
What's your question?

What's your question?
Forum: Bioinformatics 09-02-2014, 12:32 AM
Replies: 18
Views: 4,239
Posted By woodydon
Can't be more admiring...

Can't be more admiring...
Forum: RNA Sequencing 07-27-2014, 01:59 AM
Replies: 1
Views: 639
Posted By woodydon
Any suggestions or comments? Woody

Any suggestions or comments?

Woody
Forum: RNA Sequencing 07-24-2014, 09:49 PM
Replies: 21
Views: 8,586
Posted By woodydon
Question Dear all, If you use RiboZero, will...

Dear all,

If you use RiboZero, will non-polyA RNAs dominate the RNA-Seq library? My friend told me that non-polyA RNAs are highly abundant. Will RiboZero end up dilute the polyA RNAs, which should...
Forum: RNA Sequencing 07-24-2014, 12:20 AM
Replies: 1
Views: 639
Posted By woodydon
Only 10% of the RiboZero RNA-Seq reads are from polyA+ RNAs?

Dear all,

My friend told me that the illumina RiboZero will capture mostly non-polyA transcripts. The mRNA transcripts will be only 10% of the total reads. Could you please share a little bit...
Forum: Genomic Resequencing 07-23-2014, 06:38 PM
Replies: 4
Views: 1,469
Posted By woodydon
Hi Richard, I like your comments. My tumor...

Hi Richard,

I like your comments. My tumor samples are a rare type of cancer which is not included in TCGA's collection. I have tried to substrate dbSNP and 1000 genomes (GMAF > 0), and I still...
Forum: Genomic Resequencing 07-22-2014, 12:48 AM
Replies: 4
Views: 1,469
Posted By woodydon
Any suggestions?

Any suggestions?
Forum: Genomic Resequencing 07-17-2014, 11:07 PM
Replies: 4
Views: 1,469
Posted By woodydon
Cancer Exome-Seq data without matched Normal

Dear all,

I am aware of that tumor exome-seq data without matched normal will have difficulty for distinguishing somatic and germline mutations. I aim to find "important" somatic mutations from...
Forum: Bioinformatics 06-24-2014, 06:41 PM
Replies: 112
Views: 38,685
Posted By woodydon
My command was: ~/bbmap/ecc.sh threads=8...

My command was:

~/bbmap/ecc.sh threads=8 -Xmx14g in=~/reads/n_R1
.fastq out=~/reads/n_eccR1.fastq

Ecc.sh's log:


Settings:
threads: 8
Forum: Bioinformatics 06-24-2014, 04:06 PM
Replies: 112
Views: 38,685
Posted By woodydon
Question Hi Brain, I used ecc.sh to correct my raw...

Hi Brain,

I used ecc.sh to correct my raw .fq files and then use bbmerge.sh again. I found the assemble rate is much lower:

Reads: 136095860
Joined: 13084199 9.614%...
Forum: Bioinformatics 06-23-2014, 07:15 PM
Replies: 112
Views: 38,685
Posted By woodydon
Wink I see~ thanks for GenoMax's and your...

I see~ thanks for GenoMax's and your explanations!

Woody
Forum: Bioinformatics 06-23-2014, 12:29 AM
Replies: 112
Views: 38,685
Posted By woodydon
Wink I can't find error-correcting option in...

I can't find error-correcting option in bbmerge.sh. Also, in bbmap.sh, "out=" seems outputs reads instead of sam files. Could you please give me a hint? Thanks!
Forum: Bioinformatics 06-22-2014, 11:16 PM
Replies: 112
Views: 38,685
Posted By woodydon
Hi Brian, Thank you for the quick reply. It...

Hi Brian,

Thank you for the quick reply. It indeed was the problem of not finding java. I have consulted with the administrator about this since I used java before without a problem.

Sincerely,...
Forum: Bioinformatics 06-22-2014, 10:31 PM
Replies: 112
Views: 38,685
Posted By woodydon
Unhappy Hi Brain, I am using a computing cluster to...

Hi Brain,

I am using a computing cluster to run BBMerge and found the following error:



my command was:
Forum: Bioinformatics 06-18-2014, 07:10 PM
Replies: 112
Views: 38,685
Posted By woodydon
Wink Great. That's an neat option.

Great. That's an neat option.
Forum: Bioinformatics 06-17-2014, 11:48 PM
Replies: 112
Views: 38,685
Posted By woodydon
Wink Thanks for the reply. It turns out that I...

Thanks for the reply. It turns out that I confused your "insert size" with "inner distance" of pair-end reads. Since the ~25 million reads were exome-seq data, 44.594% assemble rate is a bit lower...
Forum: Bioinformatics 06-17-2014, 01:10 AM
Replies: 112
Views: 38,685
Posted By woodydon
Is there a list of parameters that I can use? For...

Is there a list of parameters that I can use? For example, insert size and cpu threads. I tried to assembled a set of ~24 million pair-end reads and found that only 44.59% were assembled. Is there a...
Forum: Ion Torrent 06-16-2014, 07:32 PM
Replies: 9
Views: 8,113
Posted By woodydon
Unhappy Why would you spend money on PGM? PGM data is bad...

Why would you spend money on PGM? PGM data is bad and is known to have homopolymer problems for a long time. However, the company claimed that they have their way to fix the homopolymer problem by...
Forum: RNA Sequencing 04-17-2014, 07:34 PM
Replies: 0
Views: 562
Posted By woodydon
Smile About SureSelect custom DNA and RNA kit

Dear all,

Is there a difference between SureSelect custom DNA and RNA kit?

Bests,
Woody
Forum: Bioinformatics 04-09-2014, 11:32 PM
Replies: 14
Views: 4,090
Posted By woodydon
Thanks for the reply. Do you see only very...

Thanks for the reply.

Do you see only very rare mutations? Or you see other relatively more abundant mutations that are unlikely to be germline mutations. If there are more abundant somatic...
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