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Search: Posts Made By: Elsie
Forum: Bioinformatics 03-14-2017, 05:45 PM
Replies: 2
Views: 3,349
Posted By Elsie
A bit late, sorry, but I believe this can be done...

A bit late, sorry, but I believe this can be done by converting these files to PLINK format, and then using PLINK/SEQ (https://atgu.mgh.harvard.edu/plinkseq/output.shtml)
Forum: General 03-09-2016, 12:38 PM
Replies: 1
Views: 1,751
Posted By Elsie
That is such a thoughtful offer BillShannon, I am...

That is such a thoughtful offer BillShannon, I am sure that it has helped many scientists.
Forum: Bioinformatics 11-16-2015, 12:01 PM
Replies: 17
Views: 1,656
Posted By Elsie
Thank you so much for the ppt - that is very...

Thank you so much for the ppt - that is very helpful.
This tool will be incredibly useful in our trouble-shooting toolkit - thank you so much for not only making it available, but for putting in the...
Forum: Bioinformatics 11-15-2015, 05:20 PM
Replies: 17
Views: 1,656
Posted By Elsie
Hi Brian, Is it possible to obtain some...

Hi Brian,

Is it possible to obtain some further information on this program, e.g. how exactly it works?, the columns of the results.txt file?

Many thanks.
Forum: Bioinformatics 11-15-2015, 05:14 PM
Replies: 17
Views: 1,656
Posted By Elsie
java -Xmx20m -version java version "1.7.0_67" ...

java -Xmx20m -version
java version "1.7.0_67"
Java(TM) SE Runtime Environment (build 1.7.0_67-b01)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)


No java error and a complete...
Forum: Bioinformatics 11-15-2015, 04:36 PM
Replies: 17
Views: 1,656
Posted By Elsie
java -Xmx20m -version java version...

java -Xmx20m -version

java version "1.6.0_34"
OpenJDK Runtime Environment (IcedTea6 1.13.6) (rhel-1.13.6.1.el6_6-x86_64)
OpenJDK 64-Bit Server VM (build 23.25-b01, mixed mode)

We do have...
Forum: Bioinformatics 11-12-2015, 01:49 AM
Replies: 17
Views: 1,656
Posted By Elsie
Works a treat. All my transcripts are still...

Works a treat.
All my transcripts are still remaining, which validates my hypothesis that there is no (or no substantial) cross talk.
Got 1 java error running cross block:

Rename/Merge Phase...
Forum: Bioinformatics 11-10-2015, 12:20 PM
Replies: 17
Views: 1,656
Posted By Elsie
Brian you are a genius. I'll give this a go and...

Brian you are a genius.
I'll give this a go and let you know what the results look like, thank you.
Forum: Bioinformatics 11-09-2015, 11:50 AM
Replies: 17
Views: 1,656
Posted By Elsie
Ah no reference genomes unfortunately, part of...

Ah no reference genomes unfortunately, part of the problem.
Forum: Bioinformatics 11-09-2015, 11:36 AM
Replies: 17
Views: 1,656
Posted By Elsie
Multiplexing ~20 samples of different, complex...

Multiplexing ~20 samples of different, complex organisms, on the MiSeq. No red flags but it would be nice to know if there were any good methods for eliminating/investigating possible cross-talk....
Forum: Bioinformatics 11-09-2015, 12:45 AM
Replies: 17
Views: 1,656
Posted By Elsie
Thanks Brian, Genomax and sarvidsson for the...

Thanks Brian, Genomax and sarvidsson for the helpful comments. Do you feel that this methodology would remove all possible cross-talk?
thanks.
Forum: Bioinformatics 09-21-2015, 01:13 PM
Replies: 5
Views: 1,341
Posted By Elsie
Thanks for the comments Brian. 100bp PE, belong...

Thanks for the comments Brian.
100bp PE, belong to the Hymenoptera order. Current evidence is pointing towards Polydnaviruses.
Forum: Bioinformatics 09-20-2015, 03:18 PM
Replies: 5
Views: 1,341
Posted By Elsie
Thanks Smurali. These are field samples, not...

Thanks Smurali.

These are field samples, not inbred. Everything is pointing towards a virus being integrated into the chromosome. Will do some more work on this and if I find out anything useful,...
Forum: Bioinformatics 09-16-2015, 03:18 PM
Replies: 5
Views: 1,341
Posted By Elsie
Genome assembly - 2 similar samples - one good, one bad

Hi, currently doing genome assemblies on 2 very similar samples.

- 1 assembled brilliantly very quickly.
- 1 is highly fragmented

Any reason why one sample should behave so differently from...
Forum: RNA Sequencing 03-30-2015, 01:02 PM
Replies: 2
Views: 1,864
Posted By Elsie
Ribo-zero - FastQC plots - Per sequence GC content

Dear all

Running Ribo-zero kits on human data, seen consistent FastQC plots like this.
Looks like a few very highly expressed ncRNAs, a result of the kit producing far more variable coverage and...
Forum: Vendor Forum 03-30-2015, 12:50 PM
Replies: 108
Views: 51,725
Posted By Elsie
Hi Brian, My plots look similar, slightly...

Hi Brian,
My plots look similar, slightly better than yours, but I have decided to postpone posting them as we are moving to V2 chemistry in a few weeks. I'll redo the plots then and post them....
Forum: Vendor Forum 03-09-2015, 02:50 PM
Replies: 108
Views: 51,725
Posted By Elsie
Thanks Brian. BBmap is currently running, I'll...

Thanks Brian. BBmap is currently running, I'll post the results. By the way, I always want to type bbduck...
thanks.
Forum: Vendor Forum 03-09-2015, 01:07 PM
Replies: 108
Views: 51,725
Posted By Elsie
Hi GenoMax, Your dumb question was,...

Hi GenoMax,

Your dumb question was, unfortunately, spot on - interleaved is fine but trimmed is tiny - hard to map when there is nothing to map! I'll double check this, thank you.
Forum: Vendor Forum 03-09-2015, 11:32 AM
Replies: 108
Views: 51,725
Posted By Elsie
Hi Brian, hi Genomax, thanks for the...

Hi Brian, hi Genomax,

thanks for the replies.
Brian - that was just a typo by me, it was the correct file.
Genomax - I am after stats.
I'm just on my way into work, 6.30am here, I'll log on...
Forum: Vendor Forum 03-09-2015, 01:54 AM
Replies: 108
Views: 51,725
Posted By Elsie
No error, just Nas which is why I think I am...

No error, just Nas which is why I think I am missing something:
reformat.sh in1=R1.fastq in2=R2.fastq out=interleaved
gzip interleaved
bbmap.sh ref=hg19.fa
bbduk.sh in=interleaved.gz...
Forum: Vendor Forum 03-06-2015, 02:10 AM
Replies: 108
Views: 51,725
Posted By Elsie
Hi Brian, sorry, still having issues. I've now...

Hi Brian,
sorry, still having issues. I've now switched to some NextSeq data generated with mouse and human data. I'm getting Nas in my histograms, I think there is something wrong with my index,...
Forum: Vendor Forum 03-03-2015, 04:39 PM
Replies: 108
Views: 51,725
Posted By Elsie
Thank you Brian, that is really helpful, and...

Thank you Brian, that is really helpful, and incredibly prompt. Thank you so much.
Forum: Vendor Forum 03-03-2015, 04:36 PM
Replies: 108
Views: 51,725
Posted By Elsie
Thanks Brian, unfortunately I do not have a...

Thanks Brian, unfortunately I do not have a reference for this sequence!, so I'm assuming no way around this?
Forum: Vendor Forum 03-03-2015, 04:28 PM
Replies: 108
Views: 51,725
Posted By Elsie
Hi Brian, Thanks so much for this. I am...

Hi Brian,

Thanks so much for this. I am trying to repeat your above commands, using interleaved files, and I get this error, can you help?
Thanks.

bbmap.sh maxindel=200 in=trimmed.fq.gz...
Forum: Bioinformatics 10-24-2014, 04:50 PM
Replies: 4
Views: 1,918
Posted By Elsie
clarissaboschi - no idea sorry, I'd suggest...

clarissaboschi - no idea sorry, I'd suggest contacting the VEP authors directly with a reproducible/detailed example - good luck.
Showing results 1 to 25 of 85

 


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