Myrna questions

[Rachelly]

Hi all,
Two small questions about myrna:

1) I didn't understand how the per gene p-values and q-values are calculated. The p-valuse represent the significance of a gene having a certain gene expression level by the amount of reads mapped to it? By the score of the alignment?

2) I'm trying to run myrna with bowtie-args "--sam" to get a SAM file of the alignment, and get this error (it works just fine with the same parameters without the flag "bowtie-args").
Any ides why this happens?

* sh: line 1: 18915 Segmentation fault /home/sbsuser/bin/bowtie-0.12.7/bowtie --partition 1000000 --mm -t --hadoopout --st
artverbose --sam --12 .tmp.Align.pl.18662.LOG-sub1-lane8 /data/BKU/Runs/2.7-Dec-10/Lif****z/myrna_dir/jar/index/tomato 2> .tmp.
Align.pl.18662.LOG-sub1-lane8.err
* cp * /tmp/error/Align.pl.18662/
* cp: cannot stat `*': No such file or directory
* cp .* /tmp/error/Align.pl.18662/
* cp: omitting directory `.'
* cp: omitting directory `..'
* /home/sbsuser/bin/bowtie-0.12.7/bowtie exited with non-zero exitlevel 35584; see /tmp/error/Align.pl.18662 on Pipeline

Thanks,
Rachelly.

[hsmart]

Dear All,

Myrna software: http://bowtie-bio.sourceforge.net/myrna/index.shtml
I am trying to use Myrna software to analyze RNA-seq data from two cell-lines. We repeated experiments twice for each of the cell line hence I merged the data from repeated experiments. However, I am getting an error message while using following command:
myrna_local --input=Cell1_ Cell2.manifest --preprocess --reference=MYRNA_REFS/human_ensembl_58 --output=output_full --cpus=8 --intermediate=~/intermediate --keep-all --quality=phred64 --family=poisson --tempdir=~/temp

I am getting following error message:
Normalization: lup
Output URL: /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count
Processing label Normal-Subject1-Lane1/2
stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/Normal-Subject1-Lane1/2.txt >& /dev/null
stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/Normal-Subject1-Lane1/2.norm >& /dev/null
stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/Normal-Subject1-Lane1/2.norms >& /dev/null
mv: cannot move `.tmp.Normal.pl.29153' to `Normal-Subject1-Lane1/2.txt': No such file or directory
stat /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/2.txt >& /dev/null
cp Normal-Subject1-Lane1/2.txt /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/ >&2
cp: cannot stat `Normal-Subject1-Lane1/2.txt': No such file or directory
Can't load Normal-Subject1-Lane1/2.txt to /gs1/users/rakesh/CIT/Analysis/Myrna/intermediate/count/ (256)

The Cell1_ Cell2.manifest file details are:
/data/rakesh/CIT/Analysis/Myrna/Cell1_F_combined.txt 0 /data/rakesh/CIT/Analysis/Myrna/Cell1_R_combined.txt 0 Normal-Subject1-Lane1
/data/rakesh/CIT/Analysis/Myrna/Cell2_F_combined.txt 0 /data/rakesh/CIT/Analysis/Myrna/Cell2_R_combined.txt 0 Tumor-Subject1-Lane1

Can you please help me to solve the issue?

I really appreciate your help,

Thanks,

Rakesh