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Forum: Bioinformatics 07-13-2016, 01:39 AM
Replies: 0
Views: 893
Posted By ty23991
Arrow Duplicates removal on analysis-ready bam file with duplicates marked

Hi pals,
I have already preprocessed bam file that has duplicates marked, realigned and BQSR performed by GATK.
Because of some reasons, I need to remove the duplicates.

Is it a good idea to...
Forum: Bioinformatics 07-05-2016, 12:02 PM
Replies: 5
Views: 2,296
Posted By ty23991
I checked my unfiltered vcf files but could not...

I checked my unfiltered vcf files but could not find any with normal and tumor both with mutant genotype. So mutant does not seem to output germline at all.

Mutect also uses a filtering criterion...
Forum: Bioinformatics 07-01-2016, 06:35 AM
Replies: 5
Views: 2,296
Posted By ty23991
Yes. I agree. But I m not sure what filters can I...

Yes. I agree. But I m not sure what filters can I use for the germline variants .
Forum: Bioinformatics 07-01-2016, 06:13 AM
Replies: 5
Views: 2,296
Posted By ty23991
Mutect is good for somatic variant calls, not the...

Mutect is good for somatic variant calls, not the germline.
Forum: Bioinformatics 06-30-2016, 04:22 PM
Replies: 5
Views: 2,296
Posted By ty23991
Germline variant calling using tumor-normal pairs in GATK

Hi
i have tumor normal pairs and am interested in calling germline variants. The GATK UnifiedGenotyper does seem to call the germline variants as it does not require normal/tumor input arguments.
...
Forum: Bioinformatics 03-18-2016, 05:10 PM
Replies: 2
Views: 1,733
Posted By ty23991
Preprocessing the exome seq bam file for copy number estimation

Hi all,

There are known limitations involved in the copy number estimation from exome sequencing (Tumor/Normal).

For instance the following paper provides some insights.
Teo et al....
Forum: Bioinformatics 02-11-2016, 03:09 PM
Replies: 5
Views: 1,263
Posted By ty23991
That is for sure a normal practice. I am...

That is for sure a normal practice. I am wondering why sometimes single read alignment yields better alignment rate compared to paired end alignment ?
Forum: Bioinformatics 02-11-2016, 12:54 PM
Replies: 5
Views: 1,263
Posted By ty23991
I used bowtie2 I have two separate bam files....

I used bowtie2
I have two separate bam files. If i understand your suggestion correctly, i align those files (converting them to fastq) and run the paired reads alignment. right ?
Forum: Bioinformatics 02-11-2016, 12:04 PM
Replies: 5
Views: 1,263
Posted By ty23991
Enable pairing in a bam file separately aligned by lanes

Hi all,
I aligned paired end exome seq R1 and R2 fastq files separately as single end reads. Then I combined two resultant bam files using samtools cat and then sorted them by sequence.

However,...
Forum: Bioinformatics 02-11-2016, 11:54 AM
Replies: 5
Views: 1,813
Posted By ty23991
Thanks all for the suggestions. I changed the...

Thanks all for the suggestions.
I changed the tool used for trimming. I shifted to cutadapt - performed trimming for adapters and by base quality.

Finally i got the rates of alignment for the...
Forum: Bioinformatics 01-27-2016, 01:51 PM
Replies: 5
Views: 1,813
Posted By ty23991
Thanks Here is the command: bowtie2...

Thanks
Here is the command:
bowtie2 --phred33 -x HG19 -N 0 -I 60 -1 sbx.R1_trimmed.fastq.gz -2 sbx.R2_trimmed.fastq.gz -S sbx_hg19_x.sam -p 16
Forum: Bioinformatics 01-27-2016, 11:28 AM
Replies: 5
Views: 1,813
Posted By ty23991
Arrow Poor alignment rate by bowtie2 for exome sequence data

Hi
I am aligning the paired exome sequencing data, that originated from

Sorted raw data bam file -->
Converted to fastq -->
Trimmed for adapters and quality -->
Alignment using bowtie2.
...
Forum: Bioinformatics 06-22-2015, 01:22 PM
Replies: 4
Views: 951
Posted By ty23991
Thanks for the idea. I am thinking to perform the...

Thanks for the idea. I am thinking to perform the alignment on both with and without trimming and compare the results.
Forum: Bioinformatics 06-22-2015, 12:25 PM
Replies: 4
Views: 951
Posted By ty23991
Hi Brian Thanks for the suggestion. Here...

Hi Brian
Thanks for the suggestion.

Here is the trimming report:

Trimming was performed by using 1 prefix pairs, 10 forward/reverse sequences

Input Read Pairs: 532073495
Both Surviving:...
Forum: Bioinformatics 06-22-2015, 11:34 AM
Replies: 4
Views: 951
Posted By ty23991
Arrow New k-mers overpresentation by adapter trimming

Hi
I am working on an Illumina Hiseq paired end whole genome data.

The data shows overrepresentation of adapter sequences such as TruSeq Adapter, Index 14 (97% over 40bp) according to the...
Forum: Bioinformatics 05-26-2015, 04:21 PM
Replies: 3
Views: 2,108
Posted By ty23991
Thanks so much. It turned out that the output...

Thanks so much. It turned out that the output directory was located in a different file system in a cluster and that somehow causes bedtools output to be written at extremely slow rate. The problem...
Forum: Bioinformatics 05-26-2015, 01:09 PM
Replies: 3
Views: 2,108
Posted By ty23991
Arrow bedtools bamtofastq taking too long

Hi
I am running the bedtools bamtofastq for converting bam to splitted fastq (read1 and read2) files for paired end reads with an expected wall time of 24 hours and memory of 4000mb.

The input ...
Forum: Bioinformatics 05-18-2015, 10:46 AM
Replies: 0
Views: 1,252
Posted By ty23991
Arrow Filtering bowtie2 output sam file by mismatch number

Hi
I got a sam file output from bowtie2 by choosing option -N (setting number of mismatches allowed in a seed alignment during multis alignment)

I used to following command.
bowtie2 --phred33...
Forum: Illumina/Solexa 05-13-2015, 02:07 PM
Replies: 7
Views: 2,240
Posted By ty23991
Thanks so much for the explanation.

Thanks so much for the explanation.
Forum: Illumina/Solexa 05-13-2015, 01:45 PM
Replies: 7
Views: 2,240
Posted By ty23991
Hi Brian, This is a sequencing experiment of...

Hi Brian,
This is a sequencing experiment of couple of cancer cell lines as available.

Read fragmentation was performed by using the standard Illumina GAII protocol, using exonuclease,...
Forum: Illumina/Solexa 05-12-2015, 05:09 PM
Replies: 7
Views: 2,240
Posted By ty23991
Thanks so much for the suggestion. Will get...

Thanks so much for the suggestion.
Will get back with the outcome.
Forum: Illumina/Solexa 05-12-2015, 03:52 PM
Replies: 7
Views: 2,240
Posted By ty23991
Thanks Brian No custom primer was used. The...

Thanks Brian
No custom primer was used.
The sequencing was performed based on standard TrueSeq library
Forum: Bioinformatics 05-12-2015, 03:37 PM
Replies: 0
Views: 887
Posted By ty23991
Arrow Installation of bowtie2 with multithreading failed

Hi

I am in need of running the bowtie2 with enabled multithread option on a linux cluster. I do not have the root access.

I installed the tool as follows:


unzip...
Forum: Illumina/Solexa 05-12-2015, 03:27 PM
Replies: 7
Views: 2,240
Posted By ty23991
Arrow Illumina HiSeq k-mers

Hi
This is about the Illumina Hiseq based on Trueseq library.

Prior to trimming, the fastqc showed some k-mers enrichment in the middle and 5' end.

I performed the following
- quality...
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