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Search: Posts Made By: jp.
Forum: RNA Sequencing 07-24-2015, 02:22 AM
Replies: 3
Views: 2,025
Posted By jp.
Thank you Michael for solving my trouble you...

Thank you Michael for solving my trouble
you are the leader :)
Forum: RNA Sequencing 07-22-2015, 06:50 AM
Replies: 3
Views: 2,025
Posted By jp.
ops.. I also want that DESeq2 treats samples as...

ops.. I also want that DESeq2 treats samples as replicates but it doesnt as attached
Forum: Bioinformatics 07-17-2015, 09:19 AM
Replies: 4
Views: 1,602
Posted By jp.
Thanks westerman, however, I like to ask you...

Thanks westerman, however, I like to ask you something different but relative.
After running Denovo Trinity reports Trinity.fasta and then I did blast got blastx.outfmt6. I also have TransDecoder...
Forum: Bioinformatics 07-16-2015, 02:24 AM
Replies: 2
Views: 2,962
Posted By jp.
Hi I have the same problem. How can I...

Hi
I have the same problem.
How can I replace Trinity gene numbers to real gene names ?
I have blast hits file from TransDecoder of Trinity.
My question is that how to run DEG to get real gene...
Forum: Bioinformatics 07-16-2015, 02:18 AM
Replies: 4
Views: 1,602
Posted By jp.
Hi Any solution of your problem ? I am...

Hi
Any solution of your problem ?
I am confused with too
Forum: Bioinformatics 08-15-2014, 10:26 PM
Replies: 5
Views: 3,011
Posted By jp.
Smile Thank you mclo41 Yes, I did compete my run...

Thank you mclo41
Yes, I did compete my run using command lines on my server and these were just warnings on cummRbunds, So, I just ignored then because there were not errors....
Thank you again
jp
Forum: Bioinformatics 08-05-2014, 11:09 PM
Replies: 5
Views: 3,011
Posted By jp.
Question I got the same error : Warning messages: 1:...

I got the same error :
Warning messages:
1: attributes are not identical across measure variables; they will be dropped

Did you get any solution?? please let me know...
Second thing, I think...
Forum: Bioinformatics 07-14-2014, 09:52 PM
Replies: 5
Views: 2,525
Posted By jp.
Can you explain how did you solve error in blast ...

Can you explain how did you solve error in blast
I have downloaded blast and all database and kept in NCBI-blast****/db

What is next to do with it ??
thank you
Forum: Bioinformatics 07-13-2014, 02:40 AM
Replies: 4
Views: 2,117
Posted By jp.
Can you please post solution.. I have same error ...

Can you please post solution.. I have same error
thank you
Forum: Bioinformatics 05-15-2014, 09:56 PM
Replies: 2
Views: 1,306
Posted By jp.
Question I m also searching the same tools. Is there...

I m also searching the same tools.
Is there anybody who got the answer ?
thank you
Forum: Bioinformatics 05-06-2014, 05:55 AM
Replies: 3
Views: 2,998
Posted By jp.
Question anybody got answer? My trouble is to make...

anybody got answer?
My trouble is to make csHeatmap of normalized diff gene's fpkm values.
For example, csHeatmap can be generated using XLOC IDs (cummeRbund gets the real fpkm values and makes...
Forum: RNA Sequencing 05-05-2014, 01:38 AM
Replies: 4
Views: 3,511
Posted By jp.
I shifted to gplots. cummeRbund gives lot scale...

I shifted to gplots.
cummeRbund gives lot scale and without normalization, it is not accepted for publication. I dont know how to normalise using R. Therefore, I mannualy normalized values and...
Forum: Bioinformatics 04-27-2014, 10:21 PM
Replies: 2
Views: 906
Posted By jp.
did any one get answer? which stage blat should...

did any one get answer?
which stage blat should be used? .bam files or after annovar for mutations in exome seq?
thank you
Forum: Bioinformatics 04-27-2014, 10:19 PM
Replies: 5
Views: 4,332
Posted By jp.
Hi all I m doing exome seq mutation using...

Hi all
I m doing exome seq mutation using PICAR+GATK followed by annovar. I have successfully completed the pipelines and got my resuts. However, I want to filter out my SNPs using blat??
can some...
Forum: Bioinformatics 04-09-2014, 03:31 AM
Replies: 3
Views: 8,536
Posted By jp.
I need help here from experts, really apreaciate...

I need help here from experts, really apreaciate it...I tried enough but I cant do it. this one
http://seqanswers.com/forums/showthread.php?t=33023&highlight=heatmap.2
Forum: Bioinformatics 04-09-2014, 03:30 AM
Replies: 4
Views: 1,133
Posted By jp.
can somebody answer this trouble, please? ...

can somebody answer this trouble, please?
http://seqanswers.com/forums/showthread.php?t=33023&highlight=heatmap.2
Forum: Bioinformatics 04-09-2014, 03:30 AM
Replies: 10
Views: 6,443
Posted By jp.
hi all Can somebody expain me to add five...

hi all
Can somebody expain me to add five different colors in heatmap.2 (gplots). for example:
I have nine different values (-1 -0.8 -0.5 -0.2 0 0.2 0.5 0.8 1) and I want nine colors of my choice...
Forum: Bioinformatics 04-08-2014, 09:16 PM
Replies: 3
Views: 26,976
Posted By jp.
Question hi all I got the same error which is "Error in...

hi all
I got the same error which is "Error in hclustfun(distfun(if (symm) x else t(x))) :
NA/NaN/Inf in foreign function call (arg 11)".
I have multiple missing values and I have entered NA....
Forum: Bioinformatics 04-06-2014, 03:47 AM
Replies: 9
Views: 15,186
Posted By jp.
I am using...

I am using GenomeAnalysis-3.1-1/GenomeAnalysisTK.jar -T BaseRecalibrator --defaultBaseQualities 1; is it okay ? My samples are from PE101 Illumina of Cancer Cell lines with no normal control.
My...
Forum: Bioinformatics 03-25-2014, 12:59 AM
Replies: 7
Views: 1,962
Posted By jp.
Question I tried using MuTect output .bam.out to convert...

I tried using MuTect output .bam.out to convert into avinput, however, the format was not proper and I got no annotations after annovar. Moreover, when I used sed '/REJCT/d' input.bam.out >...
Forum: Bioinformatics 03-19-2014, 06:19 PM
Replies: 22
Views: 7,474
Posted By jp.
Question Yes, I did the same as mentioned by tophat...

Yes, I did the same as mentioned by tophat manual. My dir structure is:
$ pwd
$ ./wd
$ ls
ncbi-blast-2.2.29+ blast tophat_sample_Lung1
$ cd blast
$ ls
nr nt and contains all files...
Forum: Bioinformatics 03-19-2014, 04:55 PM
Replies: 22
Views: 7,474
Posted By jp.
Question Let me thank u first, and read permissions are: ...

Let me thank u first, and read permissions are:
$ pwd
$ ./wd
$ ls -l ./wd/blast
total 4328832
-rwxrwxr-x 1 jp jp 43599965 Jan 15 15:37 ensGene.txt
-rwxrwxr-x 1 jp jp 1078 Jan 15 15:37...
Forum: Bioinformatics 03-18-2014, 07:00 PM
Replies: 22
Views: 7,474
Posted By jp.
Question I think so that pre-built db needs only PATH. and...

I think so that pre-built db needs only PATH. and I did as follows:
dir structure
PATH=$PATH:wd/ncbi-blast-2.2.29+/bin
PATH=$PATH:wd/blast
PATH=$PATH:wd/blast/nr
PATH=$PATH:wd/blast/nt...
Forum: Bioinformatics 03-17-2014, 11:54 PM
Replies: 22
Views: 7,474
Posted By jp.
Question I m sorry for not mentioning exactly before. The...

I m sorry for not mentioning exactly before. The blast executable was downloaded from here only: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...blast+/2.2.29/ for linux64 bit. However, I dont have problem in...
Forum: Bioinformatics 03-17-2014, 06:00 AM
Replies: 22
Views: 7,474
Posted By jp.
Question Yes, I have downloaded from there only all the...

Yes, I have downloaded from there only all the database.
But the problem is that I dont know how to make database, the files are there in the exact PATH but program can not find it cos database is...
Showing results 1 to 25 of 142

 


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