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Forum: Bioinformatics 04-05-2013, 06:17 AM
Replies: 8
Views: 43,210
Posted By SEQond
I find Illumina's explanation for paired-end...

I find Illumina's explanation for paired-end quite lacking. Wikipedia has a better explanation (http://en.wikipedia.org/wiki/Paired-end_tag)
Forum: Bioinformatics 01-16-2013, 06:26 AM
Replies: 0
Views: 1,023
Posted By SEQond
young and old L1 subfamilies, Repeat Elements

I am interested to find which subfamilies of L1 elements belong to which "age" group. So far I have not found any such categorisation.

For instance I have found through literature that L1Pa2 is...
Forum: Bioinformatics 12-03-2012, 08:00 AM
Replies: 3
Views: 2,911
Posted By SEQond
Also interested in this

Also interested in this
Forum: Bioinformatics 10-12-2012, 05:54 AM
Replies: 36
Views: 18,917
Posted By SEQond
With this same method one can get the sequence in...

With this same method one can get the sequence in fasta format also so you can build a Bowtie index.

Instead of "GTF" choose "sequence" to get the FASTA.

As a side not remember that with the...
Forum: Bioinformatics 10-09-2012, 04:28 AM
Replies: 36
Views: 18,917
Posted By SEQond
There should be a way to minimize time allocated...

There should be a way to minimize time allocated for RefGenome mapping by throwing out the fragments that align to rRNA, tRNA or mtGenes by filtering out prior to the alignment to the refGenome, and...
Forum: Bioinformatics 10-08-2012, 07:56 AM
Replies: 36
Views: 18,917
Posted By SEQond
Interesting topic mart555 How did you do the...

Interesting topic
mart555 How did you do the integration? Just cat or anything more?

Thanks
Forum: Bioinformatics 09-28-2012, 04:14 AM
Replies: 0
Views: 975
Posted By SEQond
Over representation testing on repeat element subclass terms

Hi all,

I have UCSC tracks that after processing show subclass terms of a particular class of repeat elements.

Is there a software that can access online UCSC and check immediately for...
Forum: Bioinformatics 08-02-2012, 06:16 AM
Replies: 3
Views: 1,649
Posted By SEQond
Possibly bowtie 2 is the answer to the issue ...

Possibly bowtie 2 is the answer to the issue

also look here (http://seqanswers.com/forums/showthread.php?t=3790) or here (http://seqanswers.com/forums/showthread.php?t=17397)
Forum: Bioinformatics 07-27-2012, 04:56 AM
Replies: 3
Views: 1,649
Posted By SEQond
Can ELAND in this way align Paired End sequences...

Can ELAND in this way align Paired End sequences while at the same time masking selectively bases of only a one of the two reads?

To be honest I would prefer a BW based aligner (Bowtie,BWA, and...
Forum: RNA Sequencing 07-26-2012, 02:10 AM
Replies: 0
Views: 1,440
Posted By SEQond
Mask x number of bases WITHIN sequence prior to alignment

Hi all,

As you may see from the picture I have this QC from all R2 reads of my Paired End sequenced samples. Due to a technical error during the sequencing I am ending up with 30+ R2 reads with...
Forum: Bioinformatics 07-26-2012, 01:42 AM
Replies: 3
Views: 1,649
Posted By SEQond
Mask x number of bases WITHIN sequence prior to alignment

Message moved to correct section
http://seqanswers.com/forums/showthread.php?t=22014

Hi all,

As you may see from the picture I have this QC from all R2 reads of my Paired End sequenced...
Forum: Bioinformatics 05-22-2012, 07:20 AM
Replies: 13
Views: 5,820
Posted By SEQond
I had the same error. I removed the -sam and used...

I had the same error. I removed the -sam and used only bam as output and it worked without the segmentaton error. If later you need to convert the bam to sam there is always BEDTOOLS
Forum: Bioinformatics 04-02-2012, 12:55 AM
Replies: 4
Views: 2,705
Posted By SEQond
CAGE pipeline software

Dario1984 do you use as a pipeline the exact software mentioned in the article 1. Takahashi, H., et al., 5' end-centered expression profiling using cap-analysis gene expression and next-generation...
Forum: RNA Sequencing 03-26-2012, 07:44 AM
Replies: 4
Views: 2,808
Posted By SEQond
I am also interested

I am also interested
Forum: Bioinformatics 12-22-2011, 03:24 AM
Replies: 14
Views: 6,598
Posted By SEQond
fine I got it by the way. In case you do not see...

fine I got it by the way. In case you do not see sthng like the one above just unzoom...
Forum: Bioinformatics 12-14-2011, 04:03 AM
Replies: 53
Views: 70,829
Posted By SEQond
By utilising BEDtools and UCSC GB I am trying to...

By utilising BEDtools and UCSC GB I am trying to get a picture like this (histogram of the bedgraph in wiggle form) http://ged.msu.edu/angus/_images/ucsc007.png

so far i have used a SORTED bam on...
Forum: Bioinformatics 12-13-2011, 11:32 AM
Replies: 2
Views: 1,950
Posted By SEQond
Which annotation source is best?RNA-seq

Hi all,
From this presentation http://chagall.med.cornell.edu/NGScourse/SeqClass03_2010.pdf
I got this image
http://www.bioinformatics.gr/refSeq.gif

but how and why is one annotation source...
Forum: Bioinformatics 12-13-2011, 11:15 AM
Replies: 14
Views: 6,598
Posted By SEQond
did you find out how to show a figure like this...

did you find out how to show a figure like this above? (green histogram in a wiggle form)
thanks
Forum: Bioinformatics 12-13-2011, 08:50 AM
Replies: 14
Views: 6,598
Posted By SEQond
Pls be so kind as to provide the solution to your...

Pls be so kind as to provide the solution to your problem as others might find it useful
Forum: Bioinformatics 12-13-2011, 07:25 AM
Replies: 6
Views: 5,291
Posted By SEQond
I would like to see a bedgraph ~120MB on UCSC GB....

I would like to see a bedgraph ~120MB on UCSC GB.

I have uploaded the bedgraph file to my ftp account, how should I formulate the submission?

The following does not work
track type=bedGraph...
Forum: Bioinformatics 12-13-2011, 05:49 AM
Replies: 53
Views: 70,829
Posted By SEQond
If possible I would like that too. Thanks

If possible I would like that too.

Thanks
Forum: Bioinformatics 12-12-2011, 06:10 AM
Replies: 6
Views: 5,470
Posted By SEQond
how do you run tophat on the SGE environment? ...

how do you run tophat on the SGE environment?

here is the contents of a shell file I use but it constantly returns error report
no such file or directory. !

#!/bin/sh
#$ -V
#$ -N...
Forum: Bioinformatics 11-18-2011, 02:59 AM
Replies: 4
Views: 3,077
Posted By SEQond
Cuffdiff Gene Expression. ideal minimum number of alignments

how to identify the ideal -c "minimum number of alignments in a locus for needed to conduct significance testing" (--min-alignment-count) to be used in cuffdiff?
Forum: Bioinformatics 11-14-2011, 06:22 AM
Replies: 5
Views: 5,179
Posted By SEQond
So anyone has an idea on how to find the ideal -c...

So anyone has an idea on how to find the ideal -c "minimum number of alignments in a locus for needed to conduct significance testing" (--min-alignment-count) ?
Forum: Bioinformatics 10-18-2011, 09:27 AM
Replies: 20
Views: 10,331
Posted By SEQond
did the Cufflinks website GTF solve the problem?

did the Cufflinks website GTF solve the problem?
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