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Search: Posts Made By: slowsmile
Forum: Academic/Non-Profit Jobs 05-15-2015, 11:34 AM
Replies: 0
Views: 571
Posted By slowsmile
Post-Doctoral Research Fellow–bioinformatics in psychiatric disorder (New York)

Neurodevelopmental disorders are a common group of developmental disabilities affecting individuals of all ages. Understanding the causes and biological mechanisms underlying these disorders is...
Forum: SOLiD 01-01-2014, 08:26 PM
Replies: 2
Views: 3,631
Posted By slowsmile
Thanks Kaiye for your suggestion However, I...

Thanks Kaiye for your suggestion

However, I am still unable to convert the SoLID bam files into Pindel compatible format with the sam2pindel function. The reads in my SoLID bam file looks like...
Forum: SOLiD 12-24-2013, 05:23 PM
Replies: 2
Views: 3,631
Posted By slowsmile
Can Pindel applied to SOLiD data?

Dear All
Just want to know if anyone has relevant experiences in calling INDELS using Pindel on SOLiD data. We used Pindel on Illumina samples (bam files) with good outcome but now when we moved to...
Forum: Genomic Resequencing 04-17-2013, 09:50 PM
Replies: 4
Views: 2,950
Posted By slowsmile
dindel how to merge library files in pooled setting

Dear all
I am new to dindel and I tried to call indels from a pool of bam files. I followed their manual, which ran smoothly until step 3 when I used the --bamFiles option to analyze all bamfiles...
Forum: Bioinformatics 08-20-2012, 09:14 AM
Replies: 4
Views: 2,173
Posted By slowsmile
noiseq, where to download hg19 gene feature length?

Dear all
This might be a very native question but I really want to find out the answer ASAP.
I am trying to use Noiseq tool on human genomic data and would like to supply the function with the file...
Forum: Bioinformatics 08-05-2012, 11:38 AM
Replies: 0
Views: 967
Posted By slowsmile
can gff2 reference used in htseq-count?

Dear all
We are recently working with E.coli plasmid and tried to summarize the gene counts from our RNA-Seq samples.
The short reads were mapped to E.coli plasmid using tophat which generated bam...
Forum: Bioinformatics 06-29-2012, 10:26 AM
Replies: 8
Views: 4,812
Posted By slowsmile
To: xy6699 Your sam file looks properly sorted...

To: xy6699
Your sam file looks properly sorted (at least from the section you posted here). The warnings may come from other unpaired reads. Did you check your alignment stats? What is the...
Forum: Bioinformatics 06-27-2012, 11:31 AM
Replies: 8
Views: 4,812
Posted By slowsmile
Thanks Simon. I forgot to add -n in the...

Thanks Simon.
I forgot to add -n in the samtools sorting process and thus messed up with SAM reads.
I re-ran the program today and this time htseq-count works fine with by-name soring.
Forum: Bioinformatics 06-26-2012, 07:17 PM
Replies: 8
Views: 4,812
Posted By slowsmile
Why HTseq warning of unfound mate pairs?

Dear all
I am using htseq-count tool to summarize gene counts from bam files generated by tophat (v 2.03) based on bowtie2. I've used this pipeline (based on bowtie1) several times with human...
Forum: Bioinformatics 06-01-2012, 02:15 PM
Replies: 8
Views: 3,551
Posted By slowsmile
In my case, edgeR and DESeq gave me 3000~5000...

In my case, edgeR and DESeq gave me 3000~5000 up-regulated genes and ~1000 down-regulated genes, while SAMseq got me 9000 up-regulated but no down-regulated ones based on FDR cutoff of 0.05.
I used...
Forum: Bioinformatics 06-01-2012, 01:55 PM
Replies: 8
Views: 3,551
Posted By slowsmile
Thanks very much. I tried the SAMseq with our two...

Thanks very much. I tried the SAMseq with our two class unpaired comparison. It resulted in a lot more significant genes than I what I get from edgeR or DESeq. Did you also experience the same...
Forum: Bioinformatics 06-01-2012, 12:56 PM
Replies: 8
Views: 3,551
Posted By slowsmile
Input data structure for SAMseq

I know this might be a silly question but since we just started using the SAMseq method from CRAN R package samr to search for differentially expressed genes between two groups, I cannot find a...
Forum: Bioinformatics 03-02-2012, 11:33 AM
Replies: 2
Views: 2,195
Posted By slowsmile
extremely large vcf file generated by GATK

Dear All
I am new to snp analysis and am recently working on GATK pipeline to identify snps on the whole genome data.

I went through the stage I raw data processing protocol recommended by GATK...
Forum: Bioinformatics 02-17-2012, 08:44 AM
Replies: 13
Views: 13,218
Posted By slowsmile
Error with MarkDuplicates in Picard

Dear All
I am still on the learning curve with the GATK tool but I encountered an error at the duplicates marking step with Picard tool.

The procedure I did is the following:

I generated bam...
Forum: Bioinformatics 02-16-2012, 12:10 PM
Replies: 5
Views: 3,895
Posted By slowsmile
Unhappy mate alignment error when running ValidateSamFile in Picard

Dear All
I am trying to identify snps using GATK tool. Their manual suggested that I shall try to validate my bam files before entering the analytic pipeline.

My samples are 100 nucleotides long...
Forum: Bioinformatics 01-03-2012, 06:54 PM
Replies: 3
Views: 2,306
Posted By slowsmile
how to identify different snps between two groups?

Dear seq members

I am fairly new to SNP analysis. In my study, I have 2 groups, treatment and control, each containing 3 biological replicates. My goal is to find different snps between the two...
Forum: Bioinformatics 12-20-2011, 08:45 AM
Replies: 0
Views: 1,261
Posted By slowsmile
Unhappy One way ANOVA using cuffdiff?

Dear All
This might be a question somewhere in their manual or has been asked and answered many times in this forum.

In my analysis, I have 3 groups (each containing 3 biological replicates) and...
Forum: Bioinformatics 12-15-2011, 07:53 AM
Replies: 1
Views: 1,808
Posted By slowsmile
Unhappy help! samtools gave me more than 500,000 snps

Dear all
I must admit that I'm a newbie in the snp calling practice. I used samtools in my analysis trying to identify SNPs from 3 human samples (belong to the same group)
I used the example code...
Forum: Bioinformatics 11-30-2011, 07:42 AM
Replies: 9
Views: 4,384
Posted By slowsmile
Unhappy cufflinks 1.2.0 version got me significantly different results than the old version

I don't know if anyone else has experienced a similar problem as I had. I am analyzing several RNAseq samples following the tophat-->cuffdiff pipeline to determine differentially expressed genes. I...
Forum: Bioinformatics 06-30-2011, 02:32 PM
Replies: 2
Views: 5,897
Posted By slowsmile
Can I use FPKM to represent gene expression

Dear All
I am a newbie to the RNA-seq data analysis field. Currently, I'm in
charge of analyzing some human NGS samples (single end) in a disease-control comparative setting. I have 10 BAM files...
Forum: Bioinformatics 06-30-2011, 08:39 AM
Replies: 1
Views: 2,217
Posted By slowsmile
Can anyone share some suggestions on this issue?...

Can anyone share some suggestions on this issue? Thanks
Forum: Bioinformatics 06-29-2011, 01:14 PM
Replies: 1
Views: 2,217
Posted By slowsmile
memory issue for cuffdiff

Dear All
I am newbie to the RNA-seq data analysis field. Currently, I'm in
charge of analyzing some human NGS samples (single end) in a disease-control comparative setting. I have 10 BAM files...
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