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Old 04-09-2012, 02:57 PM   #1
jgrzymski
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Location: west coast

Join Date: Apr 2012
Posts: 1
Default Any experience with eXpress?

Hello.
We are doing some environmental RNA sequencing from an Antarctic time series. I have some prelim data from a HI Seq run, full multiplexed flow cell. Obviously we have no reference genomes. We have good community composition from old fashioned cell counting though. We built preliminary transcripts from Oases and want to quantify how many reads are associated with each transcript from each time series point. We used bowtie2 to align the reads to the transcripts and want to use a program like eXpress to quantify the counts for each transcript. Anyone have experience or luck doing this? I ran a pre-compiled binary of eXpress over the weekend (v 0.95 for Mac OSX 10.7.3) but get no results (zero counts to each transcript).
Thanks a lot for the help/advice.


my bowtie2 results are below:


41266505 reads; of these:
41266505 (100.00%) were paired; of these:
13081944 (31.70%) aligned concordantly 0 times
5372885 (13.02%) aligned concordantly exactly 1 time
22811676 (55.28%) aligned concordantly >1 times
----
13081944 pairs aligned concordantly 0 times; of these:
429328 (3.28%) aligned discordantly 1 time
----
12652616 pairs aligned 0 times concordantly or discordantly; of these:
25305232 mates make up the pairs; of these:
11035284 (43.61%) aligned 0 times
2853293 (11.28%) aligned exactly 1 time
11416655 (45.12%) aligned >1 times
86.63% overall alignment rate
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Old 04-09-2012, 03:08 PM   #2
peromhc
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Location: Durham, NH

Join Date: Sep 2009
Posts: 108
Default

that version of eXpress does not work with bowtie2.. You can get a beta (alpha?) version from Adam (see eXpress website) for a version that will work with gapped alignment. I have used this version for similar purposes, and have found it very helpful.
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bioinformatics, bowtie2, de novo transcriptome, express

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