[galaxy-user] Bam Format
Dear all, I downloaded a file in .BAM format and want to transform it into .BED format. What can I do on Galaxy? Thanks a lot! Giuseppe ___ 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] (no subject)
Hi, I read on Readme for MACS that: For the experiment with several replicates, it is recommended to concatenate several ChIP-seq treatment files into a single file. Now, I have illumina ChipSeq data: two files for IP samples and two files for Control samples. Is It right to use Concatenate datasets (text manipulation) and then use MACS for the peaks calling? Thank you so much. Giuseppe ___ 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] Help
Hi, I read on Readme for MACS that: For the experiment with several replicates, it is recommended to concatenate several ChIP-seq treatment files into a single file. Now, I have illumina ChipSeq data: two files for IP samples and two files for Control samples. Is It right to use Concatenate datasets (text manipulation) and then use MACS for the peaks calling? Thank you so much. Giuseppe ___ 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] Chip-seq data
Hi, I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSUSSTTTUTSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTUVVWVVUVVUWVVVWWWVVV Can I convert into Fastq format?If so, how can I? Furthermore, after using Map with Bowtie for Illumina, how can I use MACS (Model-based Analysis of ChIP-Seq) if I have two files for IP samples and two files for Control samples? Thank you so much. Giuseppe ___ 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/
