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Forum: Bioinformatics 05-31-2013, 05:23 AM
Replies: 12
Views: 6,069
Posted By Tuinhof
I also have the same error message, when I use...

I also have the same error message, when I use the Homo_sapiens.GRCh37.71.dna.toplevel reference.
Does this upper/lower case issue influence the mapping/counting outcome?
Forum: Bioinformatics 05-31-2013, 04:07 AM
Replies: 11
Views: 5,962
Posted By Tuinhof
The link does not work...

The link does not work...
Forum: Bioinformatics 05-31-2013, 04:06 AM
Replies: 11
Views: 5,962
Posted By Tuinhof
Dear WWQ413, thank you for trying. I will try...

Dear WWQ413, thank you for trying. I will try this on my scaffolds.
Did you already try to submit your file generated by your script to NCBI?
Forum: RNA Sequencing 05-30-2013, 05:19 AM
Replies: 0
Views: 1,346
Posted By Tuinhof
HTseq Error occured:'need more than 10 values to unpack' in line of sam file

Dear members of SEQanwers,

I have a HTseq error, witch is not known by this forum.

Error occured in line 28113765 of file /mnt/scrap_disk_1/Eric_cold_pilot/7/accepted_hits_sorted.sam.
Error:...
Forum: Bioinformatics 01-31-2013, 12:27 AM
Replies: 11
Views: 5,962
Posted By Tuinhof
Question Sorry for the late response, I was busy with...

Sorry for the late response, I was busy with other projects.
I created 7 nucleotide sequences different with N-regions to invoke error messages. Here is the outcome of the Perl script to create an...
Forum: RNA Sequencing 01-08-2013, 03:39 AM
Replies: 11
Views: 6,207
Posted By Tuinhof
What was your command line for running single end...

What was your command line for running single end reads?
I have a running paired end command line.

The only thing I can come up with is:

tophat -o path/to/file -p 6 --library-type...
Forum: Bioinformatics 09-10-2012, 05:16 AM
Replies: 11
Views: 5,962
Posted By Tuinhof
Lightbulb Generate .AGP file for WGS submission

Hi,

I have been trying for a while to submit our WGS genome data to NCBI.
I had to overcome some obstetricals, and I'm almost there, but this last obstetrical seems to be to big for me.

I...
Forum: Pacific Biosciences 08-14-2012, 05:53 AM
Replies: 55
Views: 18,440
Posted By Tuinhof
Hi LSC, I work together with Hans Jansen, he...

Hi LSC,

I work together with Hans Jansen, he installed the previous version.
Since it is not possible to go to the pages with tutorial, i was wondering how to install the newest version?
Or can...
Forum: Bioinformatics 07-24-2012, 01:32 AM
Replies: 5
Views: 2,510
Posted By Tuinhof
I have the same problem. I have downloaded the...

I have the same problem. I have downloaded the newest version (14-06-2012) of the NCBI website, and still I get an error.
Can someone help us?
Forum: Bioinformatics 07-24-2012, 01:29 AM
Replies: 0
Views: 558
Posted By Tuinhof
Hello SeqAnswers!

Hello everyone!

I'm new at SEQanswers.com.
Let me introduce myself: I'm Nynke Tuinhof and working at ZF-screens as a Bio-informatic analyst (for more then a month now). Mostly I work with RNAseq...
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