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Forum: Sample Prep / Library Generation 07-13-2016, 09:07 AM
Replies: 9
Views: 5,182
Posted By mattarno
lsherlin@NuGEN - interesting. I used HISAT2 on a...

lsherlin@NuGEN - interesting. I used HISAT2 on a fastq file generated from your RNAseq kit for model organisms (mouse) 1-16 kit, and got exactly the same alignment results for --rna-strandedness FR...
Forum: Sample Prep / Library Generation 09-18-2015, 06:03 AM
Replies: 4
Views: 3,608
Posted By mattarno
fantastic news - thanks for the input! i'll plan...

fantastic news - thanks for the input! i'll plan it and test the barcodes/indices etc.

i'm not sure how the demultiplexing pipeline works in our sequencing core (this is the only bit I won't be...
Forum: Sample Prep / Library Generation 09-18-2015, 04:34 AM
Replies: 4
Views: 3,608
Posted By mattarno
pooling libraries across multiple lanes

Dear SEQanswers experts - I have a set of 24 samples for RNAseq. The analyses I need to do is pairwise (i.e. 12 pairs of samples) for differential gene expression. I need to run them on a single...
Forum: Bioinformatics 05-22-2015, 04:42 PM
Replies: 15
Views: 5,310
Posted By mattarno
wait...did I just not put the "\" backslashes in...

wait...did I just not put the "\" backslashes in the script at the ends of lines???

I just put them in and it's doing something different...

[2015-05-23 00:37:27] Building transcriptome files...
Forum: Bioinformatics 05-22-2015, 04:27 PM
Replies: 15
Views: 5,310
Posted By mattarno
hello - I'm stuck again. I downloaded and...

hello - I'm stuck again. I downloaded and untarred the iGenome file. trying with the above script - added in the paths, but the script trips up on the transcriptome_data/known and the bowtie2Index...
Forum: Bioinformatics 05-21-2015, 11:11 AM
Replies: 15
Views: 5,310
Posted By mattarno
that's great - thanks - it's starting to come...

that's great - thanks - it's starting to come together for me now

cheers,
matt
Forum: Bioinformatics 05-21-2015, 10:09 AM
Replies: 15
Views: 5,310
Posted By mattarno
thanks - can you point me to a resource which...

thanks - can you point me to a resource which guides me through that part, i.e. how to incorporate these files into the tophat transcriptome index process? I'm a bit lost at the moment, and I have...
Forum: Bioinformatics 05-21-2015, 08:57 AM
Replies: 15
Views: 5,310
Posted By mattarno
ok - permissions now sorted. So i tried again. I...

ok - permissions now sorted. So i tried again. I am following tophat manual for making initial tophat/bowtie indexes from my GTF file:

"For example, in order to just prepare the transcriptome...
Forum: Bioinformatics 05-21-2015, 07:07 AM
Replies: 15
Views: 5,310
Posted By mattarno
great - thanks for quick reply - i am not an...

great - thanks for quick reply - i am not an admin (and a fairly novice unix user, too). i've checked permissions on bowtie2 it says '-rwxrwx---' which i guess means user has no rights --- (last...
Forum: Bioinformatics 05-21-2015, 06:53 AM
Replies: 15
Views: 5,310
Posted By mattarno
similar bowtie version issues

hi - i am having a similar problem with versions of bowtie/bowtie2 on a server. you mentioned:

"I have changed setting to make it work."

it would be great if you could expand on that...
...
Forum: RNA Sequencing 01-26-2015, 09:04 AM
Replies: 4
Views: 3,478
Posted By mattarno
Hi Paul I was wondering whether you have...

Hi Paul

I was wondering whether you have published anything with this RNAseq data you have? Is the data publicly available yet>?


Cheers,
Matt
Forum: Bioinformatics 11-23-2012, 09:36 AM
Replies: 5
Views: 4,248
Posted By mattarno
fair enough: but it's not always clear and...

fair enough: but it's not always clear and obvious. anyway, just a minor whinge, I suppose
Forum: Bioinformatics 11-23-2012, 08:30 AM
Replies: 5
Views: 4,248
Posted By mattarno
distinguish between gigabases and gigabytes: GB?

this is potentially a very dumb question: does everyone refer to gigabytes (of memory) and gigabases (of nucleotide sequence data) both as Gb in text? Or are there differences (GB and Gb)? Either way...
Forum: Ion Torrent 10-29-2012, 05:52 AM
Replies: 122
Views: 112,943
Posted By mattarno
so it only has two lanes? is that because of...

so it only has two lanes? is that because of higher depth per indexed sample?
Forum: Ion Torrent 05-03-2012, 02:29 PM
Replies: 122
Views: 112,943
Posted By mattarno
instrument reliability

sorry to stick my oar in but I'd like to ask the forum a (perhaps naive) question regarding reliability of illumina sequencers. speaking from anecdotal experience (i.e. chatting to various illumina...
Forum: Introductions 05-03-2012, 03:27 AM
Replies: 0
Views: 615
Posted By mattarno
greetings

as suggested, i'm just saying hello. first day on seqanswers...now I just have to work out some good questions...

cheers,
Matt
KCL
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