Forum: RNA Sequencing
04-23-2015, 07:48 AM
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Replies: 2
Views: 1,423
Hi bastian,
thank you for your fast answer! ...
Hi bastian,
thank you for your fast answer!
The rRNA/tRNA reads were filtered via mapping against the reference (and not with sortMeRNA). But the tmRNA was a good point. I added it to my...
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Forum: Bioinformatics
04-23-2015, 05:40 AM
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Replies: 2
Views: 3,537
Hi Claire,
if you have downloaded the...
Hi Claire,
if you have downloaded the Rfam.cm from the Rfam website (ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/), then you only have to run cmpress on the Rfam.cm file to prepare it for cmscan...
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Forum: RNA Sequencing
04-20-2015, 03:13 AM
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Replies: 2
Views: 1,423
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Forum: Bioinformatics
02-18-2015, 05:49 AM
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Replies: 10
Views: 7,942
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Forum: Bioinformatics
02-13-2015, 07:43 AM
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Replies: 10
Views: 7,942
Hi,
I have the same problem with bowtie2:
...
Hi,
I have the same problem with bowtie2:
I have bacterial paired-end Illumina reads from a dUTP library. bowtie2 has flags for strand specificity: "summere" only mentioned the --nofw/--norc...
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Forum: RNA Sequencing
12-05-2013, 02:58 AM
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Replies: 2
Views: 2,220
Hi,
I would recommend to use the ILLUMINACLIP...
Hi,
I would recommend to use the ILLUMINACLIP command; if your fragments are short you will sequence through you fragment and into the 3' adapter. It depends on your library prep and of course of...
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Forum: 454 Pyrosequencing
06-28-2012, 06:10 AM
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Replies: 10
Views: 2,500
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Forum: 454 Pyrosequencing
06-28-2012, 05:58 AM
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Replies: 10
Views: 2,500
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Forum: 454 Pyrosequencing
06-18-2012, 03:06 AM
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Replies: 7
Views: 2,718
Do you see lower raw wells in your ampliocns...
Do you see lower raw wells in your ampliocns (Lib-L) as well?? Or do you sequence only Lib-A amplicons? We switched to Lib-L a few month ago; when I had a glance at our Lib-A Amplicon runs at that...
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Forum: 454 Pyrosequencing
06-15-2012, 07:06 AM
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Replies: 23
Views: 5,084
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Forum: 454 Pyrosequencing
06-15-2012, 06:59 AM
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Replies: 7
Views: 2,718
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Forum: Illumina/Solexa
05-21-2012, 09:46 AM
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Replies: 9
Views: 2,189
I am not sure if I get you right. Ho much is...
I am not sure if I get you right. Ho much is suitable depends on the size of your genome and the coverage you want and of course the sequencing experiment (output).
For a 2x36 bp sequencing...
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Forum: Illumina/Solexa
05-21-2012, 08:31 AM
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Replies: 9
Views: 2,189
Hi vebaev,
we had our GAIIx training last week...
Hi vebaev,
we had our GAIIx training last week and did the following: We prepared three additional libraries, two bacterial WGS and one cDNA library. In our training there was no time for index...
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Forum: 454 Pyrosequencing
04-02-2012, 01:21 AM
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Replies: 16
Views: 5,006
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Forum: 454 Pyrosequencing
04-02-2012, 01:15 AM
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Replies: 0
Views: 1,243
Lib-L enrichment primer sequence
Hi,
as it's mentioned in the subject, I am searching for the sequence for the enrichment primer for the Lib-L Adaptors. We get often more oil from roche, so that we can do more emPCRs, but we are...
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Forum: 454 Pyrosequencing
03-07-2012, 08:57 AM
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Replies: 43
Views: 12,770
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Forum: 454 Pyrosequencing
01-17-2012, 06:40 AM
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Replies: 12
Views: 6,870
We do a lot of 16S sequencing and only do...
We do a lot of 16S sequencing and only do unidirectional sequencing with the Lib-L Kit.
We also had problems after our upgrade to XL+. We compared the same libraries with Titanium and XL+...
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Forum: 454 Pyrosequencing
01-17-2012, 05:52 AM
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Replies: 15
Views: 11,258
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Forum: 454 Pyrosequencing
12-09-2011, 08:27 AM
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Replies: 19
Views: 6,672
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Forum: 454 Pyrosequencing
11-22-2011, 01:15 PM
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Replies: 15
Views: 5,017
We are sequencing unidirectional amplicons and...
We are sequencing unidirectional amplicons and processing them with the shotgun pipeline. Although it is not recomended from roche to use the Lib-A Kit we don't really see a difference in the moment...
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Forum: 454 Pyrosequencing
11-22-2011, 10:39 AM
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Replies: 15
Views: 5,017
Yep, I switched to the new protocols.
For the...
Yep, I switched to the new protocols.
For the Amplicons we are evaluating which protocol works better, Titanium or XL+. Roche recommends to use the Titanium protocol for amplicons <650bp, but...
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Forum: 454 Pyrosequencing
11-22-2011, 09:22 AM
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Replies: 15
Views: 5,017
Hi Phillip,
here a some examples:
XL+ ...
Hi Phillip,
here a some examples:
XL+
WGS: 64-68 Mb from a medium run; 26 Mbases from a M/S run.
Amplicons: varying between 18-27 from a M/S run and 34-52 from a medium run
FLX
WGS: 70-89...
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Forum: 454 Pyrosequencing
11-22-2011, 07:56 AM
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Replies: 15
Views: 5,017
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Forum: 454 Pyrosequencing
11-22-2011, 07:21 AM
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Replies: 3
Views: 2,336
Hi,
did you check, if after the second...
Hi,
did you check, if after the second melting Step the white DNA beads still cluster at the enrichment beads on the MPC?
If that is the case I would suggest to decrease the copies per bead...
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