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Search: Posts Made By: AndrewCarpenter
Forum: Literature Watch 10-14-2010, 08:35 AM
Replies: 2
Views: 5,904
Posted By AndrewCarpenter
We do not currently support SOLiD data....

We do not currently support SOLiD data. Potentially in a future release though.
Forum: Literature Watch 07-21-2010, 09:24 AM
Replies: 11
Views: 4,921
Posted By AndrewCarpenter
http://bioinformatics.oxfordjournals.org/cgi/conte...

http://bioinformatics.oxfordjournals.org/cgi/content/full/btq336/DC1
Forum: Bioinformatics 07-20-2010, 06:52 AM
Replies: 0
Views: 1,377
Posted By AndrewCarpenter
Need Reference Annotation for MCF-7 Cell Line Transcripts

Any ideas as to where I can find this?
Forum: De novo discovery 07-19-2010, 08:18 AM
Replies: 0
Views: 1,742
Posted By AndrewCarpenter
MCF-7 Cell Line Transcript Reference Annotation Needed

If you could assist in any way, I'd greatly appreciate it.

PROBLEM: I recently assembled a handful of mRNA isoforms from a collection of cDNA fragments from this cell line using cufflinks and...
Forum: Bioinformatics 07-19-2010, 07:42 AM
Replies: 3
Views: 3,627
Posted By AndrewCarpenter
Cuffcompare Output Seems Incorrect

Steps taken:

KEY:
MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)

1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam

KEY:...
Forum: Bioinformatics 07-19-2010, 07:37 AM
Replies: 1
Views: 2,319
Posted By AndrewCarpenter
Yes, just use TopHat to align your reads. The...

Yes, just use TopHat to align your reads. The aligned reads will be stored in the .sam file. Cufflinks will assemble mRNA isoforms based on this file.



Cufflinks is used to estimate isoform...
Forum: Bioinformatics 07-19-2010, 07:23 AM
Replies: 1
Views: 3,256
Posted By AndrewCarpenter
a locus (plural loci) is the specific location of...

a locus (plural loci) is the specific location of a gene or DNA sequence on a chromosome.

SOURCE: sample loci file
XLOC_000001 chr1[+]x-y - transcript_id_0


For line 1-3:
col1: locus_id (ex...
Forum: Bioinformatics 07-19-2010, 05:30 AM
Replies: 3
Views: 3,627
Posted By AndrewCarpenter
Cufflinks - 'u' Class Code - Consistently Returned

Steps taken:

KEY:
MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)

1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam

KEY:...
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