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Search: Posts Made By: CottonJack
Forum: Bioinformatics 11-26-2013, 08:03 AM
Replies: 7
Views: 3,777
Posted By CottonJack
Yes, I`m trying differnet algorithms; I am...

Yes,

I`m trying differnet algorithms; I am mapping very short sequences (20-30 bp, mostly) with quite some mismatches.

Any suggestions?

Thanks.
Forum: Bioinformatics 11-26-2013, 07:03 AM
Replies: 7
Views: 3,777
Posted By CottonJack
Somebody solved this problem? :)

Somebody solved this problem? :)
Forum: 454 Pyrosequencing 07-05-2013, 12:30 AM
Replies: 2
Views: 2,284
Posted By CottonJack
Amplicon sequencing - fusion primers ordering

Dear all,

we would like to order fusion primers for 454 GS Junior amplicon sequencing.

When consulting the manual, we are not sure if the primers need to have Phosphorothioated DNA bases on the...
Forum: Illumina/Solexa 02-11-2013, 04:24 PM
Replies: 1
Views: 1,767
Posted By CottonJack
Hi Miu, I have just experience the same...

Hi Miu,

I have just experience the same thing, fragmenting pure viral RNA. I`ve tried 6,7,8,9,10 min with this buffer and also different times (10, 15 min) with RNAse III module. Also, I always...
Forum: Illumina/Solexa 02-11-2013, 02:26 PM
Replies: 3
Views: 2,078
Posted By CottonJack
Thank you, kcchan: you`ve done it for the...

Thank you,

kcchan: you`ve done it for the directional RNA sequencing protocol?
Anyway I have to cut the library band from the gel in the last step, my fear is only that I would not be able to see...
Forum: Illumina/Solexa 02-10-2013, 11:34 AM
Replies: 3
Views: 2,078
Posted By CottonJack
Cool Low input directional viral RNA sequencing

Dear users,

I would like to use directional RNA sequencing protocol (with TrueSeq siRNA adapters) to prepare libraries from fragmented RNA of purified virus. After the fragmentation and end repair...
Forum: Illumina/Solexa 01-09-2013, 08:20 AM
Replies: 2
Views: 1,137
Posted By CottonJack
Thank you!

Thank you!
Forum: Illumina/Solexa 01-09-2013, 04:24 AM
Replies: 2
Views: 1,137
Posted By CottonJack
Post Multiplexing libraries of slightly different size

Hi everybody,

I would like to multiplex libraries of different size, in one case siRNA libraries (150 bp) and in other slightly bigger ones (around 200 bp).

Is the difference in size acceptable...
Forum: Bioinformatics 12-07-2012, 08:31 AM
Replies: 0
Views: 901
Posted By CottonJack
Unhappy MAQ pileup problem

Dear all,

I'm processing MAQ pileup file and I have a problem: the depth of coverage value, which MAQ gives me is sometimes different from the one I get just counting the characters covering the...
Forum: Bioinformatics 12-04-2012, 11:44 AM
Replies: 2
Views: 813
Posted By CottonJack
Thanl you, swbarnes2, I am just wondering if...

Thanl you, swbarnes2,

I am just wondering if there is any script, which could do this automatically?
Forum: Bioinformatics 12-04-2012, 09:31 AM
Replies: 2
Views: 813
Posted By CottonJack
position heterogenity from SAMtools pileup?

Dear users,

I would like to get report, which would give me the information what's the portion of each nucleotide, which have been mapped to each position in a ref sequence, something like:
1....
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