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Forum: Bioinformatics 02-27-2012, 03:53 AM
Replies: 29
Views: 12,234
Posted By mgg
re-pairing PE files

I remember a nice contribution from kmcarr a while back which can probably help; search for thread 10392. (incidentally I can't recommend my own contribution to that thread - it is hideously slow)
...
Forum: Bioinformatics 02-24-2012, 11:56 AM
Replies: 0
Views: 1,666
Posted By mgg
velvet assembly with non-unique reads: collapse or not?

Does the level of sequence duplication in Illumina reads affect the way velvet works?

I'm trying velvet to assembly some bacterial Illumina data. It's not doing so well, producing a lot of small...
Forum: Bioinformatics 02-08-2012, 03:09 PM
Replies: 10
Views: 13,658
Posted By mgg
FastQC,kmer content, per base sequence content: is this good enough

Hi,

I'd appreciate some advice on processing some Illumina libraries

Initial FastQC runs showed the data as not great. I've used cutadapt to trim off adapters and FastQC shows improvements to...
Forum: Bioinformatics 01-05-2012, 06:22 AM
Replies: 12
Views: 6,059
Posted By mgg
suggestions

This was nice to find: I was stuck with this exact same issue. By way of putting something back in, here are some changes I made which speeded things up & simplified the code.

These changes work...
Forum: Bioinformatics 12-29-2011, 05:28 AM
Replies: 1
Views: 3,888
Posted By mgg
cutadapt: guidance on rationale for --overlap=LENGTH values

Hi,

I'm getting up to speed with Marcel Martin's cutadapt for removing adapter sequences from Illumina libraries.

I'd appreciate some expert input on what values might be reasonable for the -O...
Forum: Bioinformatics 12-06-2011, 01:52 PM
Replies: 16
Views: 12,198
Posted By mgg
The position of these peaks in the kmer plot is a...

The position of these peaks in the kmer plot is a function of read lengths. Your reads are ~ the length of the adapter, so you've got some to the right of the plot. (my experience is solely with some...
Forum: Bioinformatics 12-06-2011, 12:51 PM
Replies: 10
Views: 10,177
Posted By mgg
seeking advice on fastx_clipper

I'm looking for for some help with fastx clipper. Despite my best (if inexperienced) efforts, it's not doing what I want. So far it's little better than random. Worse, actually, since it's not...
Forum: Bioinformatics 12-06-2011, 12:20 PM
Replies: 16
Views: 12,198
Posted By mgg
Well there was also evidence from the kmer...

Well there was also evidence from the kmer analysis, which given your 57% figure I would guess would also be the case for your dataset. But yes, column 3 & 4 were the source for my (rounded) figure....
Forum: Bioinformatics 12-06-2011, 09:03 AM
Replies: 16
Views: 12,198
Posted By mgg
The sequences attached to the Index6 TruSeq...

The sequences attached to the Index6 TruSeq Adapter may not be redundant; its more likely that only the TruSeq adapter itself is over-represented. I'd be inclined to trim these adapter sequences off,...
Forum: Bioinformatics 12-06-2011, 08:56 AM
Replies: 16
Views: 12,198
Posted By mgg
It's in the Web page, over-represented sequences,...

It's in the Web page, over-represented sequences, column3, and also available from the fastqc_data text file output.

Rgds

m
Forum: Bioinformatics 11-22-2011, 06:41 AM
Replies: 16
Views: 12,198
Posted By mgg
The numbers from egrep and FastQC are (each col...

The numbers from egrep and FastQC are (each col is a library

Adapters as % 0.48 2.93 2.31 2.45 0.93 3.90 4.43 21.20 8.60 5.77

from...
Forum: Bioinformatics 11-22-2011, 04:22 AM
Replies: 16
Views: 12,198
Posted By mgg
FastQC; overrepresented sequences versus a grep

Hi,

I have an odd observation with fastQC's figure for over-represented sequences versus the number I get out when I do a simple egrep for adapter sequences in the .fastq file.

FastQC tells me...
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