Caroline,
I've had this problem before and find that although the job 'fails', the
boxplot is actually created. If you click on the 'eye' in the boxplot
history item, you should still be able to see and save your plot.
Regards,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sain
On Tuesday, November 29, 2011, graham etherington (TSL) <
graham.ethering...@sainsbury-laboratory.ac.uk> wrote:
> Caroline,
> I've had this problem before and find that although the job 'fails', the
> boxplot is actually created. If you click on the 'eye' in the boxplot
> history item, you should s
Hello Joe,
Have you found a way to convert microbial genomes from one of the
formats available on Genbank to .GTF files? We are having similar
issues with sequenced Prochlorococcus genomes, as well as with
some of our own in-house bacterial genomes.
Thanks
Hi,
I have illumina ChipSeq data in txt format with this structure:
@HWI-EAS225:8:1:1:58#0/1
NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG
+HWI-EAS225:8:1:1:58#0/1
DMSSUSSTTTUTSRQRTTTSSSUS
@HWI-EAS225:8:1:1:1803#0/1
NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG
+HWI-EAS225:8:1:1:1803#0/1
DLSTTSKOUTRRTTS
Hi AP,
Please keep all replies on list, this will allow the community to assist and
benefit from these correspondences.
SICER requires BED input. To go from BAM to BED:
1.) Convert BAM to SAM
2.) Convert SAM to Interval (Convert SAM to interval)
3.) Convert interval to BED(6+). This can be done
To Whom It May Concern,
I am curious if there is a tool within Galaxy to generate a set of random
intervals from a particular genome similar to the "Random Intervals" tool
within the ENCODE tools? I am using the "Aggregate datapoints" tool to get
phastCons conservation scores for peaks from ChI
I have a postdoc opening in my lab that could be an excellent opportunity for
members of this list. The project is extremely cool, and will incorporate
elements of ecology and systems biology. The position is open now, and I would
like to fill it ASAP.
Charles Delwiche
Genomic basis of spec
On 19/10/11 23:31, Daniel Blankenberg wrote:
Sorry for the delay. I did try the patch out shortly after you
contributed it, but it caused the functional to fail. I was able to
fix the issue and allow the existing tests to start passing, but I've
been bogged down lately and haven't been able
Hello Soetkin,
Is your concern that the sequences will be in FASTA format (without
quality scores) instead of FASTQ format? If so, the Galaxy tool "NGS: QC
and manipulation -> Combine FASTA and QUAL into FASTQ" can create
placeholder quality values in a FASTQ file appropriate for use with NGS
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