Forum: Sample Prep / Library Generation
07-31-2018, 12:55 PM
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Replies: 3
Views: 2,331
iGenomX?
Anyone have experience/thoughts on the iGenomX Riptide system? Worth checking out..?
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Forum: Bioinformatics
11-30-2017, 10:10 AM
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Replies: 3
Views: 1,152
QIIME's split_libraries_fastq.py...
QIIME's split_libraries_fastq.py (http://qiime.org/scripts/split_libraries_fastq.html) script can probably do what you want. You can pretty easily create an index FASTQ file of your 10nt barcodes, if...
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Forum: Illumina/Solexa
07-14-2017, 03:59 PM
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Replies: 3
Views: 4,948
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Forum: Bioinformatics
07-14-2017, 03:52 PM
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Replies: 2
Views: 857
RNAstructure is another alternative: ...
RNAstructure is another alternative:
http://rna.urmc.rochester.edu/RNAstructure.html
CentroidFold is another:
https://github.com/satoken/centroid-rna-package
If you have that many sequences,...
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Forum: Bioinformatics
07-14-2017, 03:46 PM
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Replies: 34
Views: 18,589
I would caution against blindly filtering your...
I would caution against blindly filtering your metagenomic data against any database of contaminants. Ideally, you would have negative controls run alongside your samples that could be checked for...
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Forum: Illumina/Solexa
07-10-2017, 11:09 AM
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Replies: 6
Views: 1,634
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Forum: Bioinformatics
05-19-2017, 03:53 PM
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Replies: 12
Views: 3,235
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Forum: Bioinformatics
05-19-2017, 12:55 PM
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Replies: 12
Views: 3,235
Seems to me this is something you should have...
Seems to me this is something you should have taken up with your collaborators.
I would hesitate to call this malpractice, as the word has strong implications particularly in the medical field.
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Forum: Bioinformatics
04-11-2017, 10:43 AM
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Replies: 1
Views: 1,143
You can download either MFold...
You can download either MFold (http://unafold.rna.albany.edu/?q=mfold/download-mfold) or RNAfold (http://www.tbi.univie.ac.at/RNA/) as standalone software to do a batch.
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Forum: Illumina/Solexa
04-11-2017, 09:33 AM
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Replies: 2
Views: 2,261
I would tend to agree with @thermophile that...
I would tend to agree with @thermophile that custom primers would be the way to go here. If you are on a limited budget, Illumina kits tend to be quite expensive on a per-sample basis.
If you are...
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Forum: Metagenomics
04-11-2017, 09:27 AM
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Replies: 3
Views: 2,001
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Forum: Introductions
04-07-2017, 07:34 AM
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Replies: 6
Views: 1,586
Another option: ...
Another option:
http://www.sequin.xyz/about/rnaseq/
In my experience, ERCC spikes aren't very useful for normalization. See this paper:
http://www.nature.com/nbt/journal/v32/n9/full/nbt.2931.html
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Forum: Illumina/Solexa
03-23-2017, 10:03 PM
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Replies: 29
Views: 9,027
@nucacidhunter, was this an identical pool in...
@nucacidhunter, was this an identical pool in terms of bacterial biomass and complexity? We've seen variation in sequencing quality for some amplicon libraries that probably had more off-target...
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Forum: RNA Sequencing
03-13-2017, 01:35 PM
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Replies: 7
Views: 2,108
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Forum: Illumina/Solexa
03-10-2017, 09:11 AM
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Replies: 6
Views: 2,750
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Forum: Bioinformatics
03-08-2017, 08:49 AM
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Replies: 21
Views: 7,914
You might find this benchmark to be helpful: ...
You might find this benchmark to be helpful:
http://www.nature.com/articles/srep19233
My understanding is that you are better off using newer k-mer based approaches as opposed to BLAST. I've had...
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Forum: Bioinformatics
03-08-2017, 08:39 AM
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Replies: 21
Views: 7,914
Would something like kraken or CLARK not be...
Would something like kraken or CLARK not be helpful? Are you trying to assemble and annotate de novo genomes? Or trying to figure out the microbial composition and functional content? I guess my...
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Forum: Bioinformatics
03-08-2017, 08:33 AM
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Replies: 21
Views: 7,914
Out of curiosity, why are you joining the read...
Out of curiosity, why are you joining the read pairs? A lot of the metagenomics software out there now supports paired end reads as input. The metaSPAdes assembler @GenoMax mentioned requires paired...
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Forum: RNA Sequencing
02-23-2017, 08:16 AM
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Replies: 8
Views: 3,020
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Forum: RNA Sequencing
02-22-2017, 10:17 AM
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Replies: 8
Views: 3,020
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Forum: RNA Sequencing
02-22-2017, 08:12 AM
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Replies: 8
Views: 3,020
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Forum: Illumina/Solexa
02-22-2017, 08:03 AM
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Replies: 29
Views: 9,027
We did a 2x300 run for a TCR library recently....
We did a 2x300 run for a TCR library recently. Passed spec (77.5% Q30 @ 939k with 15% PhiX), but clear tailing towards the ends of both R1 and R2 as well.
I could see error rates approaching 5%...
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Forum: Bioinformatics
02-16-2017, 09:37 AM
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Replies: 1
Views: 1,204
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Forum: Bioinformatics
02-16-2017, 09:29 AM
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Replies: 2
Views: 2,357
I like the phyloseq R package: ...
I like the phyloseq R package:
https://joey711.github.io/phyloseq/
If you are new to metagenomics work, you may want to start here:
http://qiime.org/
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Forum: Epigenetics
12-21-2016, 10:10 AM
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Replies: 3
Views: 5,688
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