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Search: Posts Made By: fznajar
Forum: Bioinformatics 10-17-2019, 04:24 PM
Replies: 1
Views: 2,737
Posted By fznajar
Hi all, has anybody tried to run psiblast...

Hi all,

has anybody tried to run psiblast with -phi_pattern option? I tried the command with the pattern file as follows:

ID xerD.
PA RX[VL]Q[LM][LM]GH

and I kept getting the following...
Forum: Bioinformatics 08-22-2019, 02:12 PM
Replies: 6
Views: 565
Posted By fznajar
They mentioned to download "cygwin" for windows...

They mentioned to download "cygwin" for windows users. I am trying to find what other emulators I can use.
Thank you for your time Genomax
Forum: Bioinformatics 08-22-2019, 01:40 PM
Replies: 6
Views: 565
Posted By fznajar
I get nothing back. It just keeps running until...

I get nothing back. It just keeps running until I interrupt it.
Forum: Bioinformatics 08-22-2019, 01:25 PM
Replies: 6
Views: 565
Posted By fznajar
I did not realize edirect needs a key at command...

I did not realize edirect needs a key at command line. As an example, I am using this command:
$ esearch -db pubmed -query "Roe B" | efetch -format docum

On different note, While setting up...
Forum: Bioinformatics 08-22-2019, 11:58 AM
Replies: 6
Views: 565
Posted By fznajar
esearch stuck

Hi,
I am using esearch (part of the edirect tools) and it seems that it gets stuck without feedback. I am using version 12.0
Any suggestions?
Thank you all
Forum: Bioinformatics 02-27-2019, 01:59 PM
Replies: 0
Views: 416
Posted By fznajar
segmentation fault clustal omega

Dear all,
I've been getting a "Segmentation fault: 11" with clustal omega. Any ideas/suggestions of how to fix this error. I've been using the program form over three years with no problems....
Forum: Bioinformatics 01-15-2019, 06:13 AM
Replies: 2
Views: 604
Posted By fznajar
I use them interchangeably. If you have 8...

I use them interchangeably. If you have 8 nucleotides you automatically have 8 bp. Technically, of course, they are different.
Forum: Bioinformatics 01-09-2019, 02:10 PM
Replies: 3
Views: 852
Posted By fznajar
You are correct GenoMax. They are identical. ...

You are correct GenoMax. They are identical. Appreciate it.
Best
Forum: Bioinformatics 01-09-2019, 09:54 AM
Replies: 3
Views: 852
Posted By fznajar
Deciding how many reads map to a plasmid or to a genome

Hi all,
I have illumina genome reads for an E. coli a collaborator is studying. The prep used had a plasmid as well. I have two questions:

1) For the reads that match both (e.g. lacI gene), how...
Forum: Bioinformatics 10-23-2018, 07:14 AM
Replies: 36
Views: 4,657
Posted By fznajar
Dear all, Can iSAAC work on mac os platform?

Dear all,
Can iSAAC work on mac os platform?
Forum: Bioinformatics 06-28-2018, 05:53 AM
Replies: 1
Views: 870
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: 870
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: 1,884
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: 1,884
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: 1,884
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: 1,884
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: 1,884
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: 1,884
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: 1,320
Posted By fznajar
Thanks Genomax.

Thanks Genomax.
Forum: General 12-08-2017, 07:11 AM
Replies: 2
Views: 1,320
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: 624
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: 1,331
Posted By fznajar
Thanks GenoMax. Best

Thanks GenoMax. Best
Forum: Bioinformatics 09-27-2016, 09:30 AM
Replies: 5
Views: 1,331
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: 1,331
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: 1,304
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,
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