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Search: Posts Made By: zgtmann
Forum: Bioinformatics 12-18-2014, 12:58 PM
Replies: 3
Views: 2,223
Posted By zgtmann
awk '{print $0 >> $1".bed"}'...

awk '{print $0 >> $1".bed"}' in_bed
Forum: De novo discovery 11-11-2013, 05:55 AM
Replies: 3
Views: 4,174
Posted By zgtmann
Hi there, May I ask you, where is difference...

Hi there,

May I ask you, where is difference between RNA-Seq data and sequencing form cDNA??

Thank you,

Petr.
Forum: Bioinformatics 09-23-2013, 07:43 AM
Replies: 1
Views: 1,654
Posted By zgtmann
Hello, did you find some algorithm for...

Hello,

did you find some algorithm for extract gaps from .sam to bed? Could you post it here,please..

Thanks,

Petr.
Forum: Bioinformatics 07-15-2013, 07:04 AM
Replies: 7
Views: 2,497
Posted By zgtmann
Ok, right now I have multiple vcf file, but I...

Ok, right now I have multiple vcf file, but I dont know, how to separate it by my input BAMs :-( And I dont know how to annotate my multiple vcf file :-( Please help me somebody !!


Thank you!!
Forum: Bioinformatics 07-11-2013, 12:25 AM
Replies: 7
Views: 2,497
Posted By zgtmann
Hello mimi lupton, first thank you for fast...

Hello mimi lupton,

first thank you for fast response :-)

Ok, thats right - I have 96 BAM files (it is 96 individual patients) and when I create BAM list ( each row in my list is...
Forum: Bioinformatics 07-09-2013, 06:08 AM
Replies: 7
Views: 2,497
Posted By zgtmann
Calling variants from multiple BAM files

Hello everybody,

I am pretty new in bioinformatics and I am still learning. Sorry, if my problem is explain here, but I did not find it.. Right know I have some troubles. I have 96 FASTQ files...
Forum: Bioinformatics 07-04-2013, 06:55 AM
Replies: 3
Views: 1,999
Posted By zgtmann
Hi guys, just use GATK to generate tab from...

Hi guys,

just use GATK to generate tab from your vfc file.

MAKING TAB-DELIMITED FILE FROM VCF BY GATK

java -jar GenomeAnalysisTK.jar \
-R reference.fasta
-T VariantsToTable \
...
Forum: Bioinformatics 04-08-2013, 05:06 AM
Replies: 16
Views: 11,635
Posted By zgtmann
I already solved it...:-) I have had mistake in...

I already solved it...:-) I have had mistake in my pathway :-)
Forum: Bioinformatics 04-05-2013, 04:46 AM
Replies: 16
Views: 11,635
Posted By zgtmann
Hello everybody, I have the same problem but...

Hello everybody,

I have the same problem but I cannot solve it :-( Do you have any advice?

I couldnt even run the example bowtie (getting stared...
Forum: Bioinformatics 03-22-2013, 12:58 AM
Replies: 3
Views: 3,212
Posted By zgtmann
Thank you for reply..But it still doesnt work :-(...

Thank you for reply..But it still doesnt work :-( I have my second pc (notebook) and there is a biolinux also and it is work prefectly fine :-( I dont know, where is problem..
Forum: Bioinformatics 03-21-2013, 07:29 AM
Replies: 3
Views: 3,212
Posted By zgtmann
GALAXY on Bio-Linux

Hello all bioinformatics,

please could you help me, I am not experienced "linux guy" :-)
But I trying to run galaxy directly from my computer? I am using Bio-Linux (ubuntu distribution) and there...
Forum: Bioinformatics 03-21-2013, 07:21 AM
Replies: 5
Views: 17,362
Posted By zgtmann
Thank you very much for your help...Finally I...

Thank you very much for your help...Finally I bought intel i7 and it is pretty good and fast machine :-) I can recommend it!!!
Forum: Bioinformatics 02-25-2013, 08:53 AM
Replies: 5
Views: 17,362
Posted By zgtmann
PC Requirements for MiSeq Reporter and others softwares

Hello everybody,

Please could you help me with selection of computer for second data analysis from MiSeq (MiSeq reporter). I just need to know, if I can run MiSeq Reporter software on processor...
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