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Search: Posts Made By: JamieHeather
Forum: Bioinformatics 07-06-2015, 03:47 AM
Replies: 0
Views: 1,083
Posted By JamieHeather
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...
Forum: Bioinformatics 06-18-2015, 05:17 AM
Replies: 3
Views: 1,060
Posted By JamieHeather
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...
Forum: Bioinformatics 06-18-2015, 04:37 AM
Replies: 3
Views: 1,060
Posted By JamieHeather
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...
Forum: Bioinformatics 06-18-2015, 03:56 AM
Replies: 3
Views: 1,060
Posted By JamieHeather
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...
Forum: RNA Sequencing 01-23-2015, 05:03 PM
Replies: 14
Views: 4,368
Posted By JamieHeather
Just for future reference, this thread describes...

Just for future reference, this thread describes the same problem I was having, and this solution got me past the same block.
Forum: Bioinformatics 06-29-2014, 07:16 AM
Replies: 3
Views: 1,140
Posted By JamieHeather
Upstream of ATG of first codon and downstream of...

Upstream of ATG of first codon and downstream of last stop codon maybe?
Forum: Bioinformatics 06-23-2014, 02:39 AM
Replies: 1
Views: 2,663
Posted By JamieHeather
It looks like the output of mFold or something...

It looks like the output of mFold or something similar
Forum: Illumina/Solexa 06-06-2014, 10:06 AM
Replies: 6
Views: 2,726
Posted By JamieHeather
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.
Forum: Bioinformatics 06-03-2014, 02:36 PM
Replies: 8
Views: 3,553
Posted By JamieHeather
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...
Forum: Bioinformatics 06-02-2014, 04:19 AM
Replies: 8
Views: 3,553
Posted By JamieHeather
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...
Forum: Bioinformatics 05-31-2014, 06:58 AM
Replies: 8
Views: 3,553
Posted By JamieHeather
Woa, do you want proteins that only appear once...

Woa, do you want proteins that only appear once in a given file, or proteins that only appear in one file or the other?

Both are easily doable in bash. If it's the first one, then gringer's...
Forum: General 05-16-2014, 03:43 AM
Replies: 12
Views: 9,952
Posted By JamieHeather
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...
Forum: General 05-15-2014, 01:30 AM
Replies: 12
Views: 9,952
Posted By JamieHeather
From what to what?

From what to what?
Forum: Illumina/Solexa 05-08-2014, 07:38 AM
Replies: 3
Views: 1,051
Posted By JamieHeather
Another option is using some kind of targeted...

Another option is using some kind of targeted pulldown/bait approach, eg SureSelect, which I imagine would be relatively less cost-prohibitive for some of the smaller RNA viruses.
Forum: Bioinformatics 04-09-2014, 02:33 AM
Replies: 1
Views: 1,043
Posted By JamieHeather
Each one really measures a different thing, but...

Each one really measures a different thing, but the question is whether that aspect of diversity is what you're interested in.

Have a read of Jost's Entropy and Diversity...
Forum: Literature Watch 03-26-2014, 11:33 AM
Replies: 0
Views: 3,175
Posted By JamieHeather
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...
Forum: Sample Prep / Library Generation 03-26-2014, 11:31 AM
Replies: 1
Views: 2,229
Posted By JamieHeather
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...
Forum: Sample Prep / Library Generation 03-26-2014, 11:21 AM
Replies: 1
Views: 1,392
Posted By JamieHeather
I only use the RNA that comes off PAXgene tubes...

I only use the RNA that comes off PAXgene tubes (or similar) but I remember a discussion with people talking about the importance of mixing well/leaving long enough to allow complete lysis.

Do...
Forum: Sample Prep / Library Generation 03-19-2014, 03:52 AM
Replies: 2
Views: 1,070
Posted By JamieHeather
DNA should be fine for months at 4 degrees,...

DNA should be fine for months at 4 degrees, provided there's no nuclease contamination.
Forum: Illumina/Solexa 02-24-2014, 02:14 AM
Replies: 1
Views: 3,391
Posted By JamieHeather
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...
Forum: Bioinformatics 02-24-2014, 02:13 AM
Replies: 2
Views: 992
Posted By JamieHeather
Why don't you post the answer you found, in case...

Why don't you post the answer you found, in case someone with a similar problem finds this thread in future?
Forum: Bioinformatics 01-13-2014, 02:57 AM
Replies: 5
Views: 1,956
Posted By JamieHeather
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...
Forum: Bioinformatics 01-06-2014, 04:35 AM
Replies: 4
Views: 1,457
Posted By JamieHeather
For something like this, you can also use agrep...

For something like this, you can also use agrep to allow mismatches.
Forum: Bioinformatics 01-06-2014, 04:30 AM
Replies: 2
Views: 2,018
Posted By JamieHeather
I've not used Augustus, but either way if it were...

I've not used Augustus, but either way if it were me I'd like to be sure those Xs were representing premature stop codons or something else.

Certainly even one N in your DNA will cause ambiguous...
Forum: Sample Prep / Library Generation 11-28-2013, 02:20 AM
Replies: 4
Views: 1,838
Posted By JamieHeather
You can probably get away with just altering your...

You can probably get away with just altering your ratio of beads to sample. There's a bunch of posts on this forum and a couple of nice blog posts about purifying ladders with different ratios to see...
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