Re: [galaxy-user] ftp
On Mar 20, 2012, at 8:13 AM, Richard Mark White wrote: Hi, Is anyone else having trouble connecting to main.g2.bx.psu.edu for FTP uploads? I cannot seem to connect since yesterday. Hi Rich, It's back up now. --nate Rich ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] Tophat error
Hi David, I don't know if you are still having this problem or not, but I did a web search and found this thread on seqanswers from 2/16 that seems like a good match to the problem you were having: http://seqanswers.com/forums/showthread.php?p=65085 These scientists resolved the problem by removing the --closure-search option from the command string. On the Galaxy tool form, this is the option Use Closure Search:. which is No by default. Perhaps you set this to be Yes? I would try switching it to No to see if that solves the problem. If not, then contacting the tool authors would probably be the best next step, either at seqanswers or directly at tophat.cuffli...@gmail.com. The original guess about genome indexes was way off base, this is a python error statement. I don't believe this to be related to the Galaxy wrapper but will cc Jeremy for a second opinion. Hopefully the first option will resolve the issue! Thanks, Jen Galaxy team On 3/14/12 11:10 AM, Jennifer Jackson wrote: Hi David, You question has posted to the list now and we will be getting back to you. It didn't post immediately due to some mail mailman server issues here. This looks like a problem that came up on a local instance. Because of that, I am going to send this over to the galaxy-...@bx.psu.edu mailing list. At first glance, this appears to be a problem with the NGS genome indexes used for the target genome. These are the instructions you followed? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are used for TopHat) We will be looking at this more later today, but I wanted to get back to you, so you that you know that this doesn't need to be posted again. Thanks! Jen Galaxy team On 3/14/12 6:48 AM, David Matthews wrote: Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, inmodule sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your
Re: [galaxy-user] Cuffdiff result P and q values
Hello Ateeq, It looks like you are working with a bacterial genome. There has been some limited discussion on the Galaxy mailing list about using RNA-seq tools with circular genomes, but the best resources are probably the tool documentation itself (e.g. http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff http://cufflinks.cbcb.umd.edu/howitworks.html#hdif), the tool author's Q/A email tophat.cuffli...@gmail.com, and seqanswers.com. From a quick check, it seems that the 'not significant' result is due to the value of Test status being NOTEST. Definition in documentation link above: NOTEST (not enough alignments for testing) Hopefully this helps, Best, Jen Galaxy team On 3/19/12 11:03 AM, Ateequr Rehman wrote: Dear galaxy user After running cuffdiff on my two samples (SAM files from bowtie) i got a list with p and q values, and löast colum is saying abou significance with P value, it seems like the comparison should be significant, but in Q value is 1, and last coumn is saying not significant any one have an idea, how to interpret it , should we take any comparsion with less than 0.05 p value as significant or not tables in excel looks like it Nay help is welcome best Ateeq test_id gene_id genelocus sample_1sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant CUFF.428.1 CUFF.428- gi|190572091|ref|NC_010943.1|:1575813-1577629 q1 q2 NOTEST 171.773 605.136 -150.518588.996 3,86E-051 no CUFF.462.1 CUFF.462- gi|190572091|ref|NC_010943.1|:1680283-1681214 q1 q2 NOTEST 696.628 322.149 -111.266538.062 7,42E-031 no CUFF.635.1 CUFF.635- gi|190572091|ref|NC_010943.1|:2343969-2346219 q1 q2 NOTEST 396.469 223.951 -0.824027 476.902 1,85E-011 no CUFF.512.1 CUFF.512- gi|190572091|ref|NC_010943.1|:1840464-1843486 q1 q2 NOTEST 136.314 70.604 -0.949109 422.322 2,41E-011 no CUFF.632.1 CUFF.632- gi|190572091|ref|NC_010943.1|:2346561-2347408 q1 q2 NOTEST 351.508 167.567 -106.882415.844 3,20E-011 no CUFF.941.1 CUFF.941- gi|190572091|ref|NC_010943.1|:3664426-3665364 q1 q2 NOTEST 282.247 133.798 -10.769 412.254 3,75E-011 no CUFF.616.1 CUFF.616- gi|190572091|ref|NC_010943.1|:2301552-2303180 q1 q2 NOTEST 169.682 744.885 -118.774462.107 3,82E-011 no CUFF.617.1 CUFF.617- gi|190572091|ref|NC_010943.1|:2295763-2297758 q1 q2 NOTEST 225.933 112.178 -101.011454.517 5,49E-011 no CUFF.9.1CUFF.9 - gi|190572091|ref|NC_010943.1|:41597-42402 q1 q2 OK 1729.08 2797.07 0.693913-4.461 8,16E-010.000179474 yes CUFF.956.1 CUFF.956- gi|190572091|ref|NC_010943.1|:3665445-3669232 q1 q2 NOTEST 518.525 323.653 -0.679966 444.565 8,76E-011 no CUFF.549.1 CUFF.549- gi|190572091|ref|NC_010943.1|:2043111-2043664 q1 q2 OK 7148.23 11816.4 0.725138-421.4432,50E+000.000275446 yes CUFF.872.1 CUFF.872- gi|190572091|ref|NC_010943.1|:3489557-3490326 q1 q2 NOTEST 220.274 840.662 -13.897 416.179 3,16E+001 no CUFF.636.1 CUFF.636- gi|190572091|ref|NC_010943.1|:2348784-2352394 q1 q2 NOTEST 114.384 601.415 -0.927447 414.807 3,35E+001 no CUFF.605.1 CUFF.605- gi|190572091|ref|NC_010943.1|:2271979-2275960 q1 q2 NOTEST 217.007 133.837 -0.697264 409.373 4,24E+001 no CUFF.568.1 CUFF.568- gi|190572091|ref|NC_010943.1|:2160538-2164415 q1 q2 NOTEST 74.365 377.013 -0.980011 395.097 7,78E+001 no CUFF.597.1 CUFF.597- gi|190572091|ref|NC_010943.1|:2250029-2250918 q1 q2 NOTEST 229.389 105.246 -112.403386.937 0.000109116 1 no Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this
