Forum: Bioinformatics
07-06-2015, 03:47 AM
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Replies: 0
Views: 1,464
SeqMonk and featureCounts disagree on rRNA
This is actually a follow-up from a previous problem I had described in this post (http://http://seqanswers.com/forums/showthread.php?t=60542&highlight=seqmonk+rrna).
In this experiment we've...
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Forum: Bioinformatics
06-18-2015, 05:17 AM
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Replies: 3
Views: 1,320
I believe that was just an artifact.
I'm...
I believe that was just an artifact.
I'm not sure exactly what it was about using the custom hg19 genome (I'd just thought that was the sensible choice given that's what I used for my reference...
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Forum: Bioinformatics
06-18-2015, 04:37 AM
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Replies: 3
Views: 1,320
OK problem solved! It was something to do with...
OK problem solved! It was something to do with the way that I'd built the custom genome - when I just imported an Ensembl genome via SeqMonk and re-ran the QC the error went away (as did the presence...
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Forum: Bioinformatics
06-18-2015, 03:56 AM
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Replies: 3
Views: 1,320
SeqMonk RNAseq QC plot error (>100 exon?)
I've just started exploring SeqMonk, just looking at human total RNA-seq data to check the distribution of different types of RNA.
However, when I run the RNA-seq QC plot option I get the...
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Forum: RNA Sequencing
01-23-2015, 05:03 PM
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Replies: 14
Views: 4,767
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Forum: Bioinformatics
06-29-2014, 07:16 AM
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Replies: 3
Views: 1,381
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Forum: Bioinformatics
06-23-2014, 02:39 AM
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Replies: 1
Views: 2,977
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Forum: Illumina/Solexa
06-06-2014, 10:06 AM
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Replies: 6
Views: 2,970
You can force it to if you need to. We tried it...
You can force it to if you need to. We tried it once, but then ran up against a bit of a wall; MiSeqs handle their tiffs differently to HiSeq and GAIIs, so the available software doesn't work on them.
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Forum: Bioinformatics
06-03-2014, 02:36 PM
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Replies: 8
Views: 4,219
I'm not very fluent in Perl, but I think that...
I'm not very fluent in Perl, but I think that might do the trick.
For posterity, my approach in python would just be to make a defaultdict for each database, with the sequence strings as keys (and...
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Forum: Bioinformatics
06-02-2014, 04:19 AM
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Replies: 8
Views: 4,219
Do you expect the actual fasta sequences to be...
Do you expect the actual fasta sequences to be exact matches, but with different headers, across the two databases?
For instance if ProteinA was in database 1, and there was a fasta entry of a...
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Forum: Bioinformatics
05-31-2014, 06:58 AM
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Replies: 8
Views: 4,219
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Forum: General
05-16-2014, 03:43 AM
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Replies: 12
Views: 12,058
Are you sure you have a fastq file? IDs for a...
Are you sure you have a fastq file? IDs for a fastq should start with an '@' character. Yours appear to start with a '>', which is the format for fasta files.
I'm assuming you want to change each...
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Forum: General
05-15-2014, 01:30 AM
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Replies: 12
Views: 12,058
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Forum: Illumina/Solexa
05-08-2014, 07:38 AM
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Replies: 3
Views: 1,207
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Forum: Bioinformatics
04-09-2014, 02:33 AM
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Replies: 1
Views: 1,269
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Forum: Literature Watch
03-26-2014, 11:33 AM
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Replies: 0
Views: 3,650
Original PEG sized-DNA precipitation paper
I've just dug up what seems to be the original paper that used different concentrations of PEG to precipitate DNA based on size, and thought it might be a useful one for reference lists, especially...
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Forum: Sample Prep / Library Generation
03-26-2014, 11:31 AM
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Replies: 1
Views: 2,437
There are things like PAXgene and Tempus tubes...
There are things like PAXgene and Tempus tubes for extraction of DNA or RNA from whole blood, which just lyse everything before nucleic acid purification
That said, while RBC lack nuclei they are...
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Forum: Sample Prep / Library Generation
03-26-2014, 11:21 AM
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Replies: 1
Views: 1,573
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Forum: Sample Prep / Library Generation
03-19-2014, 03:52 AM
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Replies: 2
Views: 1,242
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Forum: Illumina/Solexa
02-24-2014, 02:14 AM
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Replies: 1
Views: 3,675
I know that some people on this forum just add...
I know that some people on this forum just add some padding nucleotides before the adapter, so you can extend the sequencing primer back into that, bringing your Tm up. I was certainly once told by...
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Forum: Bioinformatics
02-24-2014, 02:13 AM
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Replies: 2
Views: 1,231
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Forum: Bioinformatics
01-13-2014, 02:57 AM
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Replies: 5
Views: 2,242
I don't know the answer, but there's an email...
I don't know the answer, but there's an email option on the BLAST help page (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs).
You could email them and ask (and then post...
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Forum: Bioinformatics
01-06-2014, 04:35 AM
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Replies: 4
Views: 1,751
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Forum: Bioinformatics
01-06-2014, 04:30 AM
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Replies: 2
Views: 2,431
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Forum: Sample Prep / Library Generation
11-28-2013, 02:20 AM
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Replies: 4
Views: 2,018
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