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Search: Posts Made By: LizBent
Forum: Illumina/Solexa 01-29-2014, 04:24 PM
Replies: 9
Views: 3,806
Posted By LizBent
The run statistics are getting better, so I think...

The run statistics are getting better, so I think I was freaking out for no reason... I have 3.4G of data from read 1, and it's halfway through read 2 and there are 1.7G of data, so this run should...
Forum: Illumina/Solexa 01-29-2014, 05:38 AM
Replies: 9
Views: 3,806
Posted By LizBent
1067 +/- 23

1067 +/- 23
Forum: Illumina/Solexa 01-29-2014, 04:39 AM
Replies: 9
Views: 3,806
Posted By LizBent
MiSeq 600bp sequencing problem

Hi, our Genomics Center sent me a link to the MiSeq run they are doing for us with the new 600 bp chemistry - and I notice something on the run stats that scares me:

1. Yield perfect read 1:...
Forum: Bioinformatics 05-02-2013, 07:35 AM
Replies: 514
Views: 221,423
Posted By LizBent
If you are unfamiliar with a Linux command line...

If you are unfamiliar with a Linux command line interface, this tutorial may help:

http://www.linfo.org/command_line_lesson_1.html

If you still can't get Bowtie to work, I would find someone...
Forum: Bioinformatics 05-01-2013, 11:29 AM
Replies: 514
Views: 221,423
Posted By LizBent
Did you follow the installation instructions? If...

Did you follow the installation instructions? If you did, and were successful, you can type

bowtie

into the prompt and it will give you the help screen. If you were not, you will get an error....
Forum: Bioinformatics 10-12-2012, 07:35 AM
Replies: 3
Views: 1,670
Posted By LizBent
Thanks a lot- the file does seem to be corrupt (I...

Thanks a lot- the file does seem to be corrupt (I tried a different sff file and it was read OK by read_sff, so it may just be the one file) and not compressed. This makes sense now.
Forum: Bioinformatics 10-12-2012, 06:12 AM
Replies: 3
Views: 1,670
Posted By LizBent
Is there a utility to detect how sff files are compressed?

Hi all. My lab partner has given me some sff files to work with, file name format NAME.sff.

They seem to be compressed- the biopieces command read_sff does not work with them, and when I try to...
Forum: Bioinformatics 10-10-2012, 01:17 PM
Replies: 6
Views: 4,230
Posted By LizBent
Thanks so much, I will try it

Thanks so much, I will try it
Forum: Bioinformatics 10-05-2012, 06:09 AM
Replies: 6
Views: 4,230
Posted By LizBent
Hi Jackie- actually, if you BLAST the two ends of...

Hi Jackie- actually, if you BLAST the two ends of a sequence (with or without an artificial gap in the middle), you get better matches than if you BLAST just one end at a time. It is possible you'd...
Forum: Bioinformatics 10-05-2012, 05:26 AM
Replies: 6
Views: 4,230
Posted By LizBent
Concatenating paired end reads when there are missing reads

Hi all,

I am looking for a tool that can take Illumina fastq paired end reads (already trimmed and quality filtered, so that not all the read1 sequences are paired with read2 sequences, and vice...
Forum: Bioinformatics 09-28-2012, 01:08 PM
Replies: 1
Views: 952
Posted By LizBent
How to find primers using biopieces?

Hi, I'm not much of a bioinformatician, and I am trying to learn how to use biopieces, which our real bioinformatician left behind on our server. Mostly it seems straightforward, but I am stumped by...
Forum: Bioinformatics 06-01-2012, 05:41 AM
Replies: 1
Views: 1,101
Posted By LizBent
Bowtie paired read input format

Hi there, I have some fastq data that is formatted for use with Trinity, which supports unpaired reads in paired end data (that is, some sequences that are in read1.fastq are not in read2.fastq, and...
Forum: Bioinformatics 06-01-2012, 04:53 AM
Replies: 514
Views: 221,423
Posted By LizBent
Hi, Bowtie noob question here. I have some paired...

Hi, Bowtie noob question here. I have some paired read data where there are unpaired reads (that is, these reads were removed in preprocessing because they were too short, so that there are sequences...
Forum: Bioinformatics 05-09-2012, 01:40 AM
Replies: 1
Views: 1,243
Posted By LizBent
Comparing sets of contigs

Hi, I have no reference genome for my organism, and I have de novo transcriptome contigs (made from 454 and Illumina data assembled with Newbler and Trinity, respectively, then combined with Cap3)...
Forum: Bioinformatics 04-20-2012, 03:35 AM
Replies: 4
Views: 2,626
Posted By LizBent
CAP3 to merge two assemblies?

Hi there, I have two assemblies (one from Illumina data made using Trinity, one from 454 data made using Newbler) and I would like to combine them into one assembly. It was suggested that I try CAP3...
Forum: Bioinformatics 03-12-2012, 07:49 AM
Replies: 5
Views: 8,133
Posted By LizBent
One more question: does it matter if some reads...

One more question: does it matter if some reads are unpaired (that is, I have removed poor quality or too-short sequences, so not all reads are paired)? I think if this is a problem I need to specify...
Forum: Bioinformatics 03-12-2012, 07:14 AM
Replies: 5
Views: 8,133
Posted By LizBent
Hi fkrueger, Can you give me an example of...

Hi fkrueger,

Can you give me an example of the command line you would use if you had unpaired reads (like I do) in fastq format? There are a few examples in the manual, but I'm still not certain...
Forum: Bioinformatics 03-12-2012, 06:22 AM
Replies: 5
Views: 8,133
Posted By LizBent
Use of Bowtie to remove PhiX from Illumina data

I have Illumina data that was spiked with PhiX sequences as an internal control, and I'd like to make sure those sequences are removed from my data before I try assembling it. I thought of using...
Forum: Bioinformatics 03-06-2012, 04:25 AM
Replies: 6
Views: 3,375
Posted By LizBent
No idea, you might want to ask the original...

No idea, you might want to ask the original script writer, who is cited in the comments at the top of the script (and there is also a reference to another SeqAnswers thread there that might answer...
Forum: Bioinformatics 03-05-2012, 11:21 PM
Replies: 6
Views: 3,375
Posted By LizBent
This script may be useful for interleaving pairs...

This script may be useful for interleaving pairs for Velvet (and generating non-paired singleton files):
...
Forum: Bioinformatics 02-23-2012, 02:09 AM
Replies: 12
Views: 3,727
Posted By LizBent
Hi- so far I've been testing Trinity for my...

Hi- so far I've been testing Trinity for my assemblies, though I was also thinking of using the Rnnotator pipeline (JGI Galaxy server), which uses Velvet. I'm not sure I understand what you mean by...
Forum: Bioinformatics 02-22-2012, 03:25 AM
Replies: 12
Views: 3,727
Posted By LizBent
Deepak, I suggest you post your question in a...

Deepak, I suggest you post your question in a thread that is relevant- if you have a reference genome you are not doing de novo transcriptome assembly, and you are also not looking at differential...
Forum: Bioinformatics 02-21-2012, 06:16 AM
Replies: 12
Views: 3,727
Posted By LizBent
I am also going to be mapping short reads to...

I am also going to be mapping short reads to assembled contigs from multiple samples- and my strategy is to assemble the contigs together in Trinity, then map the reads to the contigs. I would assume...
Forum: De novo discovery 02-10-2012, 07:58 AM
Replies: 7
Views: 5,011
Posted By LizBent
De novo transcriptome quality metrics?

Hi everyone

I'm going to be making several de novo transcriptome assemblies (using different software), and I wish to compare them. What metrics are best for this? I don't have a reference genome....
Forum: Bioinformatics 01-27-2012, 09:02 AM
Replies: 6
Views: 24,473
Posted By LizBent
I've tried the 13-mer adapter end sequence with...

I've tried the 13-mer adapter end sequence with the FastXtoolkit (Clip), and it didn't remove any reads. However, when I use the full primer sequences, reads are clipped and removed. I'm going to try...
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