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Forum: Bioinformatics 12-18-2018, 08:18 AM
Replies: 3
Views: 1,415
Posted By ritzriya
Thank you luc.

Thank you luc.
Forum: Bioinformatics 12-17-2018, 08:18 AM
Replies: 3
Views: 1,415
Posted By ritzriya
No reply yet? :(

No reply yet? :(
Forum: Bioinformatics 12-13-2018, 01:28 PM
Replies: 3
Views: 1,415
Posted By ritzriya
Question 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
Posted By ritzriya
Arrow Dear mei404, I am facing the same...

Dear mei404,

I am facing the same problem/error. Did you find any solution to this?

Thanks in advance.
Forum: Bioinformatics 04-19-2012, 02:15 AM
Replies: 13
Views: 5,307
Posted By ritzriya
Arrow Robby, Were you able to find an answer to...

Robby,

Were you able to find an answer to your issue? I am also confused about the output format. Please post the understanding here, if any.
Forum: Bioinformatics 04-18-2012, 05:16 AM
Replies: 10
Views: 3,954
Posted By ritzriya
Arrow 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
Posted By ritzriya
Thanks a lot, Greg. Yes I downloaded the pt-1.tar...

Thanks a lot, Greg. Yes I downloaded the pt-1.tar only. I got your point. :-)
Forum: MGISEQ (FKA Complete Genomics) 04-02-2012, 12:19 AM
Replies: 7
Views: 9,492
Posted By ritzriya
Arrow 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
Posted By ritzriya
Thank you llee. I will try calling SNPs from both...

Thank you llee. I will try calling SNPs from both the read types and compare the results.
Forum: Pacific Biosciences 03-25-2012, 10:10 PM
Replies: 7
Views: 5,991
Posted By ritzriya
Hi all, I have got the answer to this doubt....

Hi all,

I have got the answer to this doubt. If you use -header while running BLASR, you will get the header names onto the output file. Sorry for posting the query too soon. :-)
Forum: Pacific Biosciences 03-21-2012, 10:05 PM
Replies: 7
Views: 5,991
Posted By ritzriya
Arrow 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
Posted By ritzriya
Question 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
Posted By ritzriya
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
Posted By ritzriya
Question 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
Posted By ritzriya
Question 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
Posted By ritzriya
Question 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
Posted By ritzriya
Question 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
Posted By ritzriya
Question Thank you gtyrelle for the clear guidance about...

Thank you gtyrelle for the clear guidance about the CG data.
Forum: Bioinformatics 03-06-2012, 12:57 AM
Replies: 27
Views: 8,988
Posted By ritzriya
Question 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
Posted By ritzriya
Question Can you please throw some light on what kind of...

Can you please throw some light on what kind of "pipeline" you are offering to call variants using CGAtools? Or other open source softwares like GATK need to be used to call variants only?

Thanks...
Forum: Bioinformatics 03-05-2012, 04:34 AM
Replies: 27
Views: 8,988
Posted By ritzriya
Question 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
Posted By ritzriya
Question 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
Posted By ritzriya
Question samtools: bam_pileup.c:112: resolve_cigar2: Assertion `s->k < c->n_cigar' failed

Hi everyone,

I have the same problem as this thread started on. I have tried to remove the padded characters by using the awk command but still I get the same error. Following is the commands I...
Forum: Bioinformatics 03-24-2011, 03:15 AM
Replies: 6
Views: 4,054
Posted By ritzriya
Question Thank you NicoBxl. But these sequences are in the...

Thank you NicoBxl. But these sequences are in the amino acid format. I wanted it in the form of ATGC otherwise I could have got it from UniProtKB. I need to carry out the alignment using the gene...
Forum: Bioinformatics 03-23-2011, 11:19 PM
Replies: 6
Views: 4,054
Posted By ritzriya
Question 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...
Showing results 1 to 25 of 49

 


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