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Forum: Bioinformatics 06-28-2018, 05:53 AM
Replies: 1
Views: 633
Posted By fznajar
clustlO

Just a follow up on my question. It seems that different versions of clusterO give slightly different results. Just upgraded to 1.2.4 and 2 or 3 of my sequence pairs identity scores changed from...
Forum: Bioinformatics 06-25-2018, 03:55 PM
Replies: 1
Views: 633
Posted By fznajar
Clustal Omega

Dear All,
Has anyone noticed that the standalone clustal omega reports slightly different percent identities than its web counterpart? It seems that the identity values from the standalone version...
Forum: Bioinformatics 06-11-2018, 02:47 PM
Replies: 9
Views: 708
Posted By fznajar
Thank you Markiyan. Yes it does take DDR3 ECC...

Thank you Markiyan.
Yes it does take DDR3 ECC RDIMM. Appreciate your suggestions. I thought SSD is not good for continuous heavy IO. Actually, I was planning on the portable 1TB USB drive. Glad...
Forum: Bioinformatics 06-09-2018, 04:20 PM
Replies: 9
Views: 708
Posted By fznajar
I agree. NCBI released the youtube video...

I agree. NCBI released the youtube video explaining how it works. I was impressed with the taxonomy. I am using in house for tests.
I will upgrade the memory of my MacPro soon.
Thanks for your...
Forum: Bioinformatics 06-08-2018, 02:14 PM
Replies: 9
Views: 708
Posted By fznajar
Here the commands outputs that worked Markiyan ...

Here the commands outputs that worked Markiyan

Darwin cbbc.lifesci.nor.ou.edu 16.7.0 Darwin Kernel Version 16.7.0: Tue Jan 30 11:27:06 PST 2018; root:xnu-3789.73.11~1/RELEASE_X86_64 x86_64...
Forum: Bioinformatics 06-08-2018, 01:49 PM
Replies: 9
Views: 708
Posted By fznajar
GenoMax. Here are the links: For the...

GenoMax. Here are the links:

For the executables:
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.8.0alpha/

For the new database the goes with it:...
Forum: Bioinformatics 06-08-2018, 01:41 PM
Replies: 9
Views: 708
Posted By fznajar
Thanks a lot Markiyan. You are correct about the...

Thanks a lot Markiyan. You are correct about the 16GB. The checksum is correct.
Forum: Bioinformatics 06-07-2018, 12:43 PM
Replies: 9
Views: 708
Posted By fznajar
Blast 2.8.0+

Hi all,
I have been getting the following error:
Error memory mapping:/Volumes/cbbc_expansion1/BLASTDB/nt.43.nnd openedFilesCount=251 threadID=0
BLAST Database error: Error pre-fetching sequence...
Forum: General 12-08-2017, 07:58 AM
Replies: 2
Views: 956
Posted By fznajar
Thanks Genomax.

Thanks Genomax.
Forum: General 12-08-2017, 07:11 AM
Replies: 2
Views: 956
Posted By fznajar
BBmap make error

Hi all,
I am trying to "make" bbmap and I am getting this error:

BandedAlignerJNI.c:1:10: fatal error: jni.h: No such file or directory

Any advice?
Thank you
Forum: Bioinformatics 05-23-2017, 10:39 AM
Replies: 0
Views: 410
Posted By fznajar
Microarray data

Hi all,
I was wondering if anybody knows how to estimate number of transcripts (abundance) from microarray data (for examples using RMA values). Is there a way to do so?

Best
Forum: Bioinformatics 09-28-2016, 02:41 PM
Replies: 5
Views: 1,103
Posted By fznajar
Thanks GenoMax. Best

Thanks GenoMax. Best
Forum: Bioinformatics 09-27-2016, 09:30 AM
Replies: 5
Views: 1,103
Posted By fznajar
I did not. I found Blast 2.5.x. I will give this...

I did not. I found Blast 2.5.x. I will give this a shot. However, the difference in the matches is stark. Could the updates in the database itself make that much difference for ITS sequences in...
Forum: Bioinformatics 09-27-2016, 09:12 AM
Replies: 5
Views: 1,103
Posted By fznajar
command line BLASTN 2.3.0+ different hits from the web blastN

Hi,
I got different matches using the command line BLASTN 2.3.0+ (- remote) option from the NCBI website BlastN! Has anybody experienced this before?
Forum: Bioinformatics 10-17-2014, 10:28 AM
Replies: 4
Views: 1,025
Posted By fznajar
I was worried that since its eukaryote, there...

I was worried that since its eukaryote, there would be few full length genes on each contig.

appreciate both of you.

Best,
Forum: Bioinformatics 10-16-2014, 12:27 PM
Replies: 4
Views: 1,025
Posted By fznajar
annotating large number of eukaryotic contigs

What is the best way to annotate large number of contains from a eukaryote. BlastX is going to take a long time. I was wondering if FgeneSH will be a better first step?
Forum: Bioinformatics 03-01-2014, 07:21 AM
Replies: 11
Views: 6,276
Posted By fznajar
Sorry for the late reply. I used nr

Sorry for the late reply. I used nr
Forum: Bioinformatics 01-14-2014, 01:10 PM
Replies: 2
Views: 876
Posted By fznajar
Thanks. It worked.

Thanks. It worked.
Forum: Bioinformatics 01-12-2014, 08:20 AM
Replies: 2
Views: 876
Posted By fznajar
BFcounter output

Hi,
I used BFcounter to get the k-mers frequency. But I cannot open the output file. The information says that the output file is a binary file that can be converted to a tab-delimited file. Any...
Forum: Bioinformatics 12-04-2012, 01:15 PM
Replies: 0
Views: 610
Posted By fznajar
EST sequence normalization

I just got my EST sequence data assembled. There is no reference genome. Just EST from different conditions. I thought simply dividing the reads for each contig (redundancy) by all the reads from...
Forum: Bioinformatics 12-04-2012, 12:50 PM
Replies: 4
Views: 2,037
Posted By fznajar
Thanks all. It turned out my fasta reference...

Thanks all. It turned out my fasta reference sequence from illumina has a format problem as each sequences is one single long line. I just had to reformat it and it worked.

Thanks again for your...
Forum: Bioinformatics 11-14-2012, 07:05 AM
Replies: 4
Views: 2,037
Posted By fznajar
Thank you seqeve. I am still getting the same...

Thank you seqeve.
I am still getting the same error above.
Best
Forum: Bioinformatics 11-13-2012, 03:00 PM
Replies: 4
Views: 2,037
Posted By fznajar
Blast to SAM

I converted my BlasyN to SAM using:

blast2sam.pl <blastN file> > <output file>

I then tried to generate a "bam" file using:

samtools view -bT <reference.fasta> <sam file> -o...
Forum: Bioinformatics 06-13-2012, 06:58 AM
Replies: 11
Views: 6,276
Posted By fznajar
I am having the exact same problem. I am not...

I am having the exact same problem. I am not sure if SEED option is even highlighted on MEGAN menu. Anybody got success so far?
Forum: Bioinformatics 04-24-2012, 08:14 AM
Replies: 4
Views: 7,936
Posted By fznajar
It seems the new fastQ files have slightly...

It seems the new fastQ files have slightly different format that fastx quality filter tool cannot recognize it. Is there anything else out there?
Thanks
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