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Forum: Bioinformatics 09-30-2015, 01:11 PM
Replies: 1
Views: 2,686
Posted By cwisch88
Looks like some cloning vector snuck in. fastqc...

Looks like some cloning vector snuck in. fastqc didn't put it into the overrepresented sequences table, but that seems to be the problem, now to figure out what it is doing there.

I figured it out...
Forum: Bioinformatics 09-30-2015, 11:47 AM
Replies: 1
Views: 2,686
Posted By cwisch88
Mate Pair QC

I've been using a combo of fastqc and cutadapt to qc some mate pair libraries we have.

This is a Truseq LT matepair library

I'm only interested in pairs that have evidence of the junction...
Forum: Pacific Biosciences 02-04-2015, 02:37 PM
Replies: 4
Views: 3,536
Posted By cwisch88
cvargasc, I wanted to respond to his still...

cvargasc,

I wanted to respond to his still unanswered question because I ran into this issue this week.

I discovered that there is an error file in the 1-overlapper directory ending with...
Forum: Bioinformatics 12-17-2013, 10:09 AM
Replies: 4
Views: 6,355
Posted By cwisch88
That is a very straightforward approach and I...

That is a very straightforward approach and I have done that in past. I was just wondering if there was something that could quickly extract the sequences without reinventing the wheel.

It looks...
Forum: Bioinformatics 12-17-2013, 09:59 AM
Replies: 4
Views: 6,355
Posted By cwisch88
Thanks

I will definitely check these out!
Forum: Introductions 12-16-2013, 02:12 PM
Replies: 2
Views: 1,672
Posted By cwisch88
Welcome! While I haven't answered many...

Welcome!

While I haven't answered many questions on this site (maybe 1?) I have found this site to be extremely helpful!
Forum: Bioinformatics 12-16-2013, 01:54 PM
Replies: 4
Views: 6,355
Posted By cwisch88
Finding 16s DNA Sequence in de novo assembled genome

From time to time I find I'm working with a bunch of de novo assemblies. I've been interested in doing some comparative genomics and perhaps making some group-specific 16s rRNA primers.

I'm just...
Forum: Bioinformatics 08-22-2013, 07:20 AM
Replies: 17
Views: 47,304
Posted By cwisch88
lhlbio, If you have the annotations for your...

lhlbio,

If you have the annotations for your reference you can collect them all in the: 'chr1:start-end' format and then run this command:

samtools view aln.sorted.bam...
Forum: Bioinformatics 10-04-2012, 08:38 AM
Replies: 17
Views: 47,304
Posted By cwisch88
Just to clarify...

Thanks swbarnes!

Using these bits allows for lots of specificity on what you want to retrieve from your alignments, it's just a little cumbersome to someone who hasn't strayed into this portion of...
Forum: Bioinformatics 10-03-2012, 12:08 PM
Replies: 17
Views: 47,304
Posted By cwisch88
Why make 3 tmp files

I've recently been asked to do the same thing that Lspoor has posted about. Why do we need 3 tmp files? Wouldn't using -f 4 retrieve all unmapped lines?

My guess would be that this keeps all the...
Forum: Bioinformatics 04-17-2012, 07:08 AM
Replies: 6
Views: 4,196
Posted By cwisch88
This morning has been productive so far, it seems...

This morning has been productive so far, it seems the removal of the -g allows the alignment to go through. So I'm wondering if my original allowed gap (6bps) is too large? I guess I'll keep...
Forum: Bioinformatics 04-17-2012, 05:38 AM
Replies: 6
Views: 4,196
Posted By cwisch88
A FASTQ has 4 lines per read. When it segfaults...

A FASTQ has 4 lines per read. When it segfaults at 25034752 it means that it has gone through 12517376 reads from reads_1 and 12517376 from reads 2. And something in the next 131072 reads makes it...
Forum: Bioinformatics 04-16-2012, 12:17 PM
Replies: 6
Views: 4,196
Posted By cwisch88
Okay well let me get the full story here. ...

Okay well let me get the full story here.

What does the command "go" do? Are these reads that you suspect to be the problem?

From what I can tell, when this happens to me I get a number like...
Forum: Bioinformatics 04-16-2012, 10:04 AM
Replies: 6
Views: 4,196
Posted By cwisch88
Did you ever find an answer to this? I'm having...

Did you ever find an answer to this? I'm having the exact same problem!
Forum: Bioinformatics 03-22-2012, 10:56 AM
Replies: 5
Views: 4,623
Posted By cwisch88
Wow, this sentence has solved a problem I have...

Wow, this sentence has solved a problem I have been having all morning.Thanks so much!
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