Forum: Bioinformatics
12-18-2018, 08:18 AM
|
|
Replies: 3
Views: 1,415
|
|
Forum: Bioinformatics
12-17-2018, 08:18 AM
|
|
Replies: 3
Views: 1,415
|
|
Forum: Bioinformatics
12-13-2018, 01:28 PM
|
|
Replies: 3
Views: 1,415
UMI tools versus bcl2fastq2
Hi All,
I just found out that bcl2fastq2 also handles adapter trimming and UMI extraction right at the level of basecall to fastq conversion. If that is available, why would anyone use UMI_tools...
|
|
Forum: Bioinformatics
05-09-2012, 02:23 AM
|
|
Replies: 26
Views: 14,186
|
|
Forum: Bioinformatics
04-19-2012, 02:15 AM
|
|
Replies: 13
Views: 5,307
|
|
Forum: Bioinformatics
04-18-2012, 05:16 AM
|
|
Replies: 10
Views: 3,954
Same error, No solution!
Hi,
I am facing the same error as tarunmishra.rsg. Following is my config file:
It gives me the following error:
I am using SVDetect 0.8 version, which is the latest. Any help would be...
|
|
Forum: MGISEQ (FKA Complete Genomics)
04-03-2012, 03:37 AM
|
|
Replies: 7
Views: 9,492
|
|
Forum: MGISEQ (FKA Complete Genomics)
04-02-2012, 12:19 AM
|
|
Replies: 7
Views: 9,492
Evidence file format
Hi all,
I was just going through the files Complete Genomics is providing as deliverables by their Cancer sequencing service.
I downloaded the data from:...
|
|
Forum: Pacific Biosciences
03-27-2012, 10:36 PM
|
|
Replies: 2
Views: 3,301
|
|
Forum: Pacific Biosciences
03-25-2012, 10:10 PM
|
|
Replies: 7
Views: 5,991
|
|
Forum: Pacific Biosciences
03-21-2012, 10:05 PM
|
|
Replies: 7
Views: 5,991
BLASR output - what does each column mean?
Hi all,
I wanted to understand the meanings of each column in the BLASR output, which looks like:
I understand that first column denotes the query name and second column denotes the subject...
|
|
Forum: Pacific Biosciences
03-18-2012, 11:11 PM
|
|
Replies: 2
Views: 3,301
Ignore CCS reads - a correct assumption?
Hi all,
As we know that Pacbio provides CLR as well as CCS reads for error correction of the long reads for any dataset. I want to know, for Variation Detection, is it okay to ignore the CCS reads...
|
|
Forum: Bioinformatics
03-12-2012, 05:50 AM
|
|
Replies: 27
Views: 8,988
Oops, thank you. I observed that there were no...
Oops, thank you. I observed that there were no headers in the new SAM file formed. Now I am able to create the BAM file successfully. Thanks again, nora.
Though this conversion of SAM to BAM is...
|
|
Forum: MGISEQ (FKA Complete Genomics)
03-07-2012, 08:29 PM
|
|
Replies: 5
Views: 3,963
Following is the GATK command I used:
...
Following is the GATK command I used:
I have tried to run -glm SNP - it works. There lies a problem only with -glm INDEL and BOTH options. I used ValidateSam from Picard to check for errors -...
|
|
Forum: MGISEQ (FKA Complete Genomics)
03-07-2012, 04:04 AM
|
|
Replies: 5
Views: 3,963
Oh, Okay. So what I finally understand is that...
Oh, Okay. So what I finally understand is that the SAM file consists of a split-up of the mate-pair read, i.e. 2 sequences of each of the mate-pair. And even if the entire SAM file consists of such...
|
|
Forum: MGISEQ (FKA Complete Genomics)
03-06-2012, 10:36 PM
|
|
Replies: 5
Views: 3,963
Inconsistencies between evidence and SAM files
Hi everyone,
The evidence2sam command which produces the SAM file, contains records/lines where a every read is repeated twice mapping to two respective different locations, such as:
Here,...
|
|
Forum: Bioinformatics
03-06-2012, 04:25 AM
|
|
Replies: 27
Views: 8,988
Hi gtyrelle,
I have understood that variants...
Hi gtyrelle,
I have understood that variants are a part of your CG deliverables. But also I want to know that the evidence2sam command which produces the SAM file, contains records/lines where a...
|
|
Forum: Bioinformatics
03-06-2012, 02:23 AM
|
|
Replies: 27
Views: 8,988
|
|
Forum: Bioinformatics
03-06-2012, 12:57 AM
|
|
Replies: 27
Views: 8,988
I converted the sam file using the awk command...
I converted the sam file using the awk command mentioned above. But for downstream analysis, I have to convert it into BAM file using samtools view. When I do the conversion, I get the following...
|
|
Forum: Bioinformatics
03-06-2012, 12:51 AM
|
|
Replies: 27
Views: 8,988
|
|
Forum: Bioinformatics
03-05-2012, 04:34 AM
|
|
Replies: 27
Views: 8,988
Hi gtyrelle,
So you mean that its not...
Hi gtyrelle,
So you mean that its not advisable to use samtools mpileup for CG data to find variants? The command "generatemasterVar" (beta) from cgatools ONLY must be used to detect SNPs and...
|
|
Forum: Bioinformatics
03-05-2012, 04:22 AM
|
|
Replies: 27
Views: 8,988
Sure. Following are the commands I used to...
Sure. Following are the commands I used to generate the SAM file and then using samtools I converted it into BAM file. I dont think this is what you are asking me, is it? Please let me know.
...
|
|
Forum: Bioinformatics
03-05-2012, 03:56 AM
|
|
Replies: 27
Views: 8,988
|
|
Forum: Bioinformatics
03-24-2011, 03:15 AM
|
|
Replies: 6
Views: 4,054
|
|
Forum: Bioinformatics
03-23-2011, 11:19 PM
|
|
Replies: 6
Views: 4,054
Download human gene sequences
Hi all,
I have been searching NCBI as well as UCSC and Ensembl. This is really getting weird but I want to download all the Genes for humans in FASTA format. I am unable to get this from any of...
|
