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Forum: Bioinformatics 12-14-2015, 08:38 AM
Replies: 0
Views: 950
Posted By sehrrot
Enriched mapping on WGS Illumina data

Hi,

I am working on WGS illumina data (100PE) and noticed that some genomics regions have enriched reads mapping than others. I had worked on WES data and understand these enriched reads came from...
Forum: Bioinformatics 08-07-2014, 09:09 PM
Replies: 2
Views: 1,655
Posted By sehrrot
command-line pathway enrichment test

Hi

I have been doing pathway analyses using Cytoscape Cluego but now I have many input files. Is there any command line tool for pathway enrichment test (e.g. KEGG, GO, REACTOME etc)?

Thanks...
Forum: Bioinformatics 06-10-2014, 04:35 AM
Replies: 5
Views: 2,703
Posted By sehrrot
Batch effect for RNAseq data

Hi all

I am pretty new to RNAseq data and currently working on RNAseq data from Brainspan database (http://brainspan.org/). The data from the database contains normalized expression values and,...
Forum: Bioinformatics 04-09-2014, 11:19 PM
Replies: 1
Views: 816
Posted By sehrrot
individual vcfs of 1000 genome

Hi all

I tried to get a vcf file of individuals from 1000 genome project. I have downloaded a multi-sample vcf of each chromosome and then select few individuals using SelectVariant, GATK. But...
Forum: Bioinformatics 03-25-2013, 04:54 AM
Replies: 0
Views: 1,267
Posted By sehrrot
Refseq ID for mRNA and protein

Hi all

I've been trying to find a gff or other table file containing both refseq mRNA ID (NM_*****) and refseq protein ID (NP_*****) and refseq gene name. I could only find separate information...
Forum: Genomic Resequencing 07-06-2012, 04:05 AM
Replies: 9
Views: 5,928
Posted By sehrrot
Hi EvilTwin Thanks for your sharing. I am...

Hi EvilTwin

Thanks for your sharing. I am guessing my sample would have the problem in sample prep or capture efficiency. Otherwise, it might be a problem in my HiSeq, as I've experienced in the...
Forum: Genomic Resequencing 07-05-2012, 04:41 PM
Replies: 9
Views: 5,928
Posted By sehrrot
Hi EvilTwin I think so. I am still waiting...

Hi EvilTwin

I think so. I am still waiting my pipeline for on-target rate and coverages. Duplicate level on Picard is around 20-25%, which is lower than FastQC one but higher than previously I've...
Forum: Genomic Resequencing 07-04-2012, 05:03 AM
Replies: 9
Views: 5,928
Posted By sehrrot
Hi EvilTwin I just got my nimblegen v3 exome...

Hi EvilTwin

I just got my nimblegen v3 exome data from the sequencer. But I am shocked when I checked the seuqence duplication level on the FastQC, which is nearly 50%... I will do mapping onward...
Forum: Genomic Resequencing 06-24-2012, 10:20 PM
Replies: 9
Views: 5,928
Posted By sehrrot
Hi Eviltwin Could you share how much...

Hi Eviltwin

Could you share how much on-target and avg coverage you get from SeqCap EZ v3?

I am about to get the result using that kit and I need a sort of comparison with other's data. I've...
Forum: Bioinformatics 06-23-2012, 10:22 PM
Replies: 0
Views: 1,826
Posted By sehrrot
varFilter -D (maximum read depth) usage

Hi all

I am using samtools mpileup for variant calling but bit confused with using -D for maximum read depth to call variants.


As my understanding, the minimum coverage (like "-d" in this...
Forum: Bioinformatics 05-06-2012, 03:21 AM
Replies: 6
Views: 8,755
Posted By sehrrot
hi elrohir610 Could you upload your...

hi elrohir610

Could you upload your bioanalyzer profile for both? I've also experienced this kind of problem, but I don't think either PCR cycles or over-sequencing is the sole reason, of course...
Forum: Bioinformatics 04-23-2012, 05:38 PM
Replies: 2
Views: 1,331
Posted By sehrrot
GATK variant calling for multiple exome

Hi all,

Currently, I am running Unified genotyper for variant calling for around 100 exomes. It's on the cluster and I found the remaining running time is aournd 3 weeks. Is there any way that I...
Forum: Sample Prep / Library Generation 03-09-2012, 02:30 AM
Replies: 41
Views: 23,952
Posted By sehrrot
One more quick post, A bit different...

One more quick post,

A bit different behaviour between GAII and Hiseq in terms of finding the cluster density and actual showing on the cluster, me and my colleague think..
Forum: Sample Prep / Library Generation 03-09-2012, 02:28 AM
Replies: 41
Views: 23,952
Posted By sehrrot
hi all 1. Kapa kit is the best option (at...

hi all

1. Kapa kit is the best option (at least to me and my colleagues). (to Tony) please check your Kapa kit's standard, then you will get nearly 100% curve (as I always did).
2. optimising...
Forum: Bioinformatics 02-27-2012, 10:16 PM
Replies: 138
Views: 64,141
Posted By sehrrot
Thanks Orr I've tried that with V2 bed file...

Thanks Orr

I've tried that with V2 bed file but got an error message



I cannot exactly understand why the format of bed files is different - ucsc bed file and nimblegen one.
Forum: Bioinformatics 02-27-2012, 06:38 PM
Replies: 138
Views: 64,141
Posted By sehrrot
thanks for the great manual. I have a short...

thanks for the great manual.

I have a short question:
I'm analysing Nimblegen exome and not sure which bed file I have to use for SNP calling. The bed file from nimblegen is not proper format...
Forum: Bioinformatics 02-24-2012, 01:50 AM
Replies: 3
Views: 4,545
Posted By sehrrot
[SNP calling, GATK] this contig isn't present in the Fasta sequence dictionar

Hi all

I've tried snp calling using GATK unifiedgenotyper but got the error message - it seems that there's a problem in fasta sequence dictionary. I am currently following <Exome analysis> in...
Forum: Bioinformatics 02-23-2012, 05:16 PM
Replies: 7
Views: 3,876
Posted By sehrrot
Hi Bukowski where can I yourindel.vcf for...

Hi Bukowski

where can I yourindel.vcf for download knownSites:indels? Is it all included in dbsnp135 vcf file?
Forum: Bioinformatics 02-23-2012, 05:07 PM
Replies: 4
Views: 3,469
Posted By sehrrot
Hi all now it's working fine after I removed...

Hi all

now it's working fine after I removed "-I" from bwa alignment process ("bwa aln -t 4 -f input.sai -I hg19 input.fastq")
Forum: Bioinformatics 02-22-2012, 08:19 PM
Replies: 4
Views: 3,469
Posted By sehrrot
Picard Error: IllegalArgumentException: Invalid fastq character:

hi all

I'm having trouble in using Picard to covert sam to bam. it seems to be halted by weird characters (I cannot type it here)
Forum: Sample Prep / Library Generation 02-12-2012, 08:24 PM
Replies: 1
Views: 2,216
Posted By sehrrot
V3 NimbleGen exome kit

Dear all,

I am looking forward to use v3 NimbleGen exome kit. But I found that blocking oligos a bit different from v2 NimbleGen exome kit for Illumina TruSeq kit.
It's bit like that a blocking...
Forum: Sample Prep / Library Generation 11-08-2011, 04:38 PM
Replies: 1
Views: 3,875
Posted By sehrrot
Library prep for 50ng input with TruSeq DNA- or RNAseq adapters?

Dear all,

I am going to process library preparation with 50 ng DNA. I am just concerning ratio of adapters:DNA input. Thus, I am considering to use adapters from TruSeq RNAseq kit, which has lower...
Forum: Sample Prep / Library Generation 11-07-2011, 06:12 PM
Replies: 5
Views: 5,252
Posted By sehrrot
Hi Phillip, We've been experiencing this...

Hi Phillip,

We've been experiencing this issue too when we did RNAseq (lower input sequencing). We can clearly read primer dimers in base-pair composition display. But a bit surprise that you did...
Forum: Sample Prep / Library Generation 11-07-2011, 06:01 PM
Replies: 6
Views: 2,871
Posted By sehrrot
though you got lower than 2nM, you would change...

though you got lower than 2nM, you would change conditions for template preparation, which should end up at 12 pM-ish. So, it would not be a problem, but you may concern that your library would have...
Forum: Illumina/Solexa 10-05-2011, 05:36 AM
Replies: 3
Views: 9,116
Posted By sehrrot
Comparing our V3 run, it's a bit worse .. (but...

Comparing our V3 run, it's a bit worse .. (but yours 850-900 k2/mm; ours 750-800 k2/mm). This is bit complex; one reason might be slightly higher cluster but should be okay as Illumina says V3 aims...
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