[galaxy-user] trimming illumina reads from 3' without considering quality score
Is it possible to trim certain number of bases from 3' end with taking into consideration quality of reads. To explain it further, I want to remove 10bases from 3 ' end of all reads and keep first forty. Thanks ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] trimming illumina reads from 3' without considering quality score
Hi Mathew, Please see the tool 'NGS: QC and manipulation - FASTQ Trimmer by column'. Make sure your data is in .fastqsanger format first - either assigned or through grooming: See FASTQ: http://wiki.galaxyproject.org/Support#Dataset_special_cases Take care, Jen Galaxy team On 5/1/13 7:29 AM, Mathew Bunj wrote: Is it possible to trim certain number of bases from 3' end with taking into consideration quality of reads. To explain it further, I want to remove 10bases from 3 ' end of all reads and keep first forty. Thanks ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Trimming and thinning of paired-end reads
Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by quality my paired-end Illumina reads. As fas as i know if i want to use FASTX-TOOLKIT i have to treat my data as single-end, trim the adapter of the forward reads first and then proceed with the reverse reads. And same thing for the filtering by quality. Right? - Can i combine forward/reverse reads in a unique file with the FASTQ joiner and then proceed with the trimming of the adapters and the filtering by quality? If i do that, am i going to be able to remove the adapters of both directions reads? Am i going to be able to keep the broken pairs? I was reading that there is another toolkit, NGS QC TOOLKIT that allows you to work with paired-end reads and keep the broken pairs after the trimming and thinning. Did anyone try it? I think that has no galaxy option... Thanks, Alicia. –– Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/ ___ 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/
[galaxy-user] trimming
Does anyone know if it is possible to trim sequencing adaptor sequences away in Galaxy? and what is the necessary format for trimming sequences? because in Clip adapter sequences I can not to see my files. thaks Diana Trejo, PhD -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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/
[galaxy-user] Trimming small RNA
Hello everybody, I have sequences of small RNA's from 18 to 35nt and accurate trim the sequences of the adapters before aligning the reads with the reference genome. Are there any tools available to it in the Galaxy? Thanks. -- Thiago Mafra Batista Biólogo Molecular Doutorando em Bioinformática - UFMG LGB - ICB/Bloco K4 sala 245 Tel Lab: (31) 3409-2628 CV: http://lattes.cnpq.br/9414909432933240 ___ 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] Trimming small RNA
Hi, This must seem like a newbie question but I cant get a clear answer. My understanding from the galaxy wiki page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_format is that all intervals in galaxy are 0 based, start inclusive end exclusive. but when i use generate pileup/filter pileup and convert to intervals, i get something like this: chr10 1056309 1056310 G C + When i look up the SNP (G--C) it is pretty clearly 1056310. Which would make the interval end inclusive. this is key because when i annotate snp's against dbSNP, i need to have the right cooridnates. Can anyone provide some guidance? Thanks! 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/
Re: [galaxy-user] Trimming small RNA
Hi Rich, That is consistent with the BED format, that is in BEDs 0 based coordinate system the SNP is at 1056309. In the more common 1 based system this translates to 1056310. If the end were inclusive the SNP would be at 1056309-1056310 in BED world, that is it would take 2 positions. The first base of a genome in BED coordinates is represented as 0-1. My quick rule of thumb for converting between coordinate systems is to add (or subtract) 1 from the start base, leave the end base alone. Jim On Sun, Sep 11, 2011 at 10:58 PM, Richard Mark White whit...@yahoo.comwrote: Hi, This must seem like a newbie question but I cant get a clear answer. My understanding from the galaxy wiki page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_formatis that all intervals in galaxy are 0 based, start inclusive end exclusive. but when i use generate pileup/filter pileup and convert to intervals, i get something like this: chr10 1056309 1056310 G C + When i look up the SNP (G--C) it is pretty clearly 1056310. Which would make the interval end inclusive. this is key because when i annotate snp's against dbSNP, i need to have the right cooridnates. Can anyone provide some guidance? Thanks! 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/
