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Search: Posts Made By: vallejov
Forum: RNA Sequencing 12-04-2013, 06:45 PM
Replies: 5
Views: 2,368
Posted By vallejov
Hi Björn, I've put quite a bit of time into...

Hi Björn,

I've put quite a bit of time into this assembly so I would rather "fix" it if possible rather than scrap it and start again. It is a de novo transcriptome assembly not a genome.

I...
Forum: RNA Sequencing 10-22-2013, 10:56 AM
Replies: 0
Views: 1,089
Posted By vallejov
Cutadapt question

Hi all,

I would like to know if I can run Cutadapt on my transcriptome assembly (not raw reads but final assembly). Does anyone have experience with this? Should I use BLAST instead? I would like...
Forum: RNA Sequencing 08-22-2013, 01:51 PM
Replies: 5
Views: 2,368
Posted By vallejov
Adatper contamination

Hello!

I ran Fastqc on my reads and didn't detect any overrepresented sequences. As a result I did not remove any adapter sequences. I did do a 12 bp head crop and then quality trimmimg to process...
Forum: RNA Sequencing 08-22-2013, 01:34 PM
Replies: 0
Views: 1,521
Posted By vallejov
Oases transcripts smaller than Velvet contigs?

Hi All,

My n50 sizes are significantly smaller after running Oases when compared to the N50 of the contigs.fa file that I generated using Velvet. For example, for kmer size 63 the N50 value of...
Forum: RNA Sequencing 04-05-2013, 02:04 PM
Replies: 0
Views: 1,159
Posted By vallejov
problems installing sim4db-can't find python.h

Hi all,

I'm trying to install sim4db and when I run the configuration.sh file I get the following errors:

WARNING: 'python' program found, but can't find include file 'Python.h' -- is python...
Forum: RNA Sequencing 04-05-2013, 01:53 PM
Replies: 3
Views: 1,181
Posted By vallejov
Thank you so much yzzhang! I tried installing...

Thank you so much yzzhang! I tried installing sim4db but am having problems when I run the configuration.sh file. It says that it can't find the python headers (python.h). Did you encounter this...
Forum: RNA Sequencing 04-05-2013, 11:21 AM
Replies: 3
Views: 1,181
Posted By vallejov
QC my de novo assembly

Hi all,

I would like to QC my de novo assembly by comparing it to an EST library (no genome sequence available) but I don't have a clue how to go about doing that! :confused: I would appreciate...
Forum: RNA Sequencing 04-05-2013, 11:10 AM
Replies: 0
Views: 2,202
Posted By vallejov
kmer content warning in FastQC

I would be so grateful if someone wouldn't mind taking a look at the kmer content graph from FastQC. This is RNA-seq data after trimming and filtering based on quality scores. My questions are: Does...
Forum: RNA Sequencing 01-21-2013, 09:01 AM
Replies: 4
Views: 5,216
Posted By vallejov
How to determine chimeras in my de novo assembly?

Hi all,

I would like to QC my de novo transcriptome assembly (no reference genome available :( ) by looking for chimeric transcripts. Ideally, I would like to calculate a % of chimeric transcripts...
Forum: RNA Sequencing 10-08-2012, 07:45 PM
Replies: 1
Views: 1,103
Posted By vallejov
Problem with FastXtool kit

I'm a complete newbie to bioinformatics and have just started analyzing my RNA-seq data (illumina HiSeq2000 100 bp reads) and have hit a snag. I'm trying to run the fastx_quality_stats and I keep...
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