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Search: Posts Made By: mikhmv
Forum: Industry Jobs! 06-30-2014, 03:58 PM
Replies: 0
Views: 3,547
Posted By mikhmv
Researcher or Post-Doctoral Researcher Bioanalytics

Overview: BioDatomics is a developer of NGS data analysis software and services. The company has a new opportunity for candidates at the post-doctoral level. The Post-Doc will create pipelines using...
Forum: Open Genomics Engine Project 05-23-2014, 06:29 AM
Replies: 0
Views: 27,691
Posted By mikhmv
BioDT-Lab. public resource for bioinformaticians

Sorry for repost. Looks like this announcement well fit to this topic

BioDatomics has launched its BioDT Labs program, which offers free,
cloud-based access for qualified bioinformaticians to...
Forum: Bioinformatics 05-23-2014, 06:24 AM
Replies: 1
Views: 1,947
Posted By mikhmv
Tutorials for a platform

Hi Everyone,

Update: we are planning to create a series of tutorials for our platform. Here is a first one: https://www.youtube.com/watch?v=9xsL-OjoitI
Forum: Bioinformatics 05-14-2014, 02:19 PM
Replies: 1
Views: 1,947
Posted By mikhmv
BioDT-Lab. public resource for bioinformaticians

BioDatomics has launched its BioDT Labs program, which offers free,
cloud-based access for qualified bioinformaticians to BioDatomics'
Hadoop-powered bioanalytics platform. BioDT Labs differs...
Forum: RNA Sequencing 11-22-2012, 04:16 AM
Replies: 16
Views: 5,297
Posted By mikhmv
solution

The help is here:
read #1 (HWI-ST993:228:C0RWJACXX:6:2316:17166:97507) does not have a matching mate in the same order (HWI-ST993:228:C0RWJACXX:6:2316:12084:97378 found instead)

The Red text...
Forum: Bioinformatics 07-05-2012, 07:17 PM
Replies: 147
Views: 56,524
Posted By mikhmv
KaiYe: Does pindel accept breakdancer files? ...

KaiYe: Does pindel accept breakdancer files?

I tried to use this command: pindel --fasta "human_g1k_v37_decoy_optimized.fasta" \
--config-file "config_1" \
--output-prefix...
Forum: RNA Sequencing 06-11-2012, 06:29 AM
Replies: 16
Views: 5,297
Posted By mikhmv
temproary solution

you can try to rename
WIGTC-HISEQ:4:1101:1155:2046#ACAGTG/2;0 to WIGTC-HISEQ:4:1101:1155:2046#ACAGTG/1;0 in the paired file.

I mean make replacement for all read names in the second file to have...
Forum: Bioinformatics 06-11-2012, 05:28 AM
Replies: 147
Views: 56,524
Posted By mikhmv
d12ajd: I think after realignment will be better....

d12ajd: I think after realignment will be better. I have seen following deletions marked as independent with the same starting position in pindel:
A-TTTTTC and
ATTT-TTC
So, you will loose this...
Forum: Bioinformatics 04-30-2012, 05:01 PM
Replies: 13
Views: 10,154
Posted By mikhmv
Error:

+1 to all of you:
I run this command:
$TOPHAT -o $DEST -C -Q --bowtie1 -p 60 -r 200 --mate-std-dev 30 --report-secondary-alignments --report-discordant-pair-alignments --coverage-search...
Forum: Bioinformatics 03-17-2012, 01:53 PM
Replies: 32
Views: 15,613
Posted By mikhmv
Pindel to Dindel

I made improved version of script.

I have a several questions to someone who know how dindel work:
1. Can we replace INV on DEL+INS?
2. Can we do the same for RPL and TD?
3. Do we need to...
Forum: Bioinformatics 03-17-2012, 10:51 AM
Replies: 32
Views: 15,613
Posted By mikhmv
convert from pindel vcf to dindel format

I ended up with following script:
cat XXXX_D.vcf | grep DEL | awk '{print $1,"\t",$2,"\t&&&"$4}'| sed -e 's/&&&./-/'> XXXX_D.dindel.del
cat XXXX_SI.vcf | grep INS | awk '{print...
Forum: Bioinformatics 03-15-2012, 06:05 PM
Replies: 147
Views: 56,524
Posted By mikhmv
Hi KaiYe, Does pindel2vcf provide quality...

Hi KaiYe,
Does pindel2vcf provide quality score?
How can I get it in vcf?
Regards,
Forum: Bioinformatics 03-13-2012, 12:22 PM
Replies: 147
Views: 56,524
Posted By mikhmv
Hi KaiYe, I have a question how can we annotate...

Hi KaiYe,
I have a question how can we annotate BreakPoints? pindel2vcf doesn't support it.

Regards
Forum: Bioinformatics 03-12-2012, 04:34 PM
Replies: 147
Views: 56,524
Posted By mikhmv
Thanks KaiYe. "o" is working well.

Thanks KaiYe.
"o" is working well.
Forum: Bioinformatics 03-10-2012, 12:03 PM
Replies: 147
Views: 56,524
Posted By mikhmv
KaiYe, I think it is a bug. I got this message...

KaiYe,
I think it is a bug. I got this message on different chromosome depend on file but error everytime after Total reads = 0.

Is it possible to fix?

Regards,
Max
Forum: Bioinformatics 03-10-2012, 11:32 AM
Replies: 147
Views: 56,524
Posted By mikhmv
Hi KaiYe, I have an error message during...

Hi KaiYe,

I have an error message during run pindel2vcf.
The executing command was:
pindel2vcf -r $REFGENOME -R hg19b37 -d 20120310 -p 5173N_TD.res -v 5173N_TD.res2.vcf
The last few lines...
Forum: Bioinformatics 03-02-2012, 07:48 AM
Replies: 147
Views: 56,524
Posted By mikhmv
It was a quick reply!!! Thanks. I have a...

It was a quick reply!!! Thanks.

I have a several more questions now.
1. Does it mean that Pindel does not check flag that this read is duplicate?
2. If you have count it independently maybe it...
Forum: Bioinformatics 03-02-2012, 06:15 AM
Replies: 147
Views: 56,524
Posted By mikhmv
Hi KaiYe, I used MarkDuplicates from Picard...

Hi KaiYe,

I used MarkDuplicates from Picard and mark duplicates but did not removed them.
I have a question does pindel need file with removed duplicates or can work with Marked ones?

Thank...
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