User contributions for Claudius E Kerth
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27 September 2017
- 07:5007:50, 27 September 2017 diff hist +12 Butlin:Unix for Bioinformatics - basic tutorial →fixed download link for example data ; comes from my Dropbox now
- 07:1807:18, 27 September 2017 diff hist −30 Butlin:Unix for Bioinformatics - advanced tutorial →fixed link to Task 1 current
- 07:1407:14, 27 September 2017 diff hist +78 Butlin:Unix for Bioinformatics - advanced tutorial →added troubleshooting tip ; fought the curly quotation mark plague
- 06:2306:23, 27 September 2017 diff hist +109 m Butlin:Unix for Bioinformatics - basic tutorial →Simple file renaming and TAB-completion
- 06:1406:14, 27 September 2017 diff hist −24 Butlin:Unix for Bioinformatics - advanced tutorial →fixed link to Task 1 in Basic Tutorial
- 06:1006:10, 27 September 2017 diff hist −16 Butlin:Unix for Bioinformatics - advanced tutorial →removed more of the curly quotes plague
- 06:0706:07, 27 September 2017 diff hist −4 m Butlin:Unix for Bioinformatics - advanced tutorial →TASK 7: I have got a text file originating from a Windows or an old Mac text editor. But when I open it in less, all lines are concatenated into one line and with repeatedly the strange ^M character in it. How can I fix this?
- 05:5205:52, 27 September 2017 diff hist +6 m Butlin:Unix for Bioinformatics - advanced tutorial →TASK 4: I have a .fastq file with raw sequences from a RAD library. How can I find out how many of the reads contain the correct sequence of the remainder of the restriction site?
- 05:4105:41, 27 September 2017 diff hist −19 m Butlin:Unix for Bioinformatics - advanced tutorial →Overview
- 05:3805:38, 27 September 2017 diff hist −5 m Butlin:Unix for Bioinformatics - advanced tutorial →fixed link to Basic tutorial
- 05:3305:33, 27 September 2017 diff hist −20 Butlin:Unix for Bioinformatics - basic tutorial →removed the curly quotes plague
- 05:2105:21, 27 September 2017 diff hist +20 m Butlin:Unix for Bioinformatics - basic tutorial →fixed link for local download of Unix_tut_sequences
- 05:1705:17, 27 September 2017 diff hist +14 Butlin:Unix for Bioinformatics - basic tutorial →fixed download link for Unix_tut_sequences.fastq.gz ; comes from my Dropbox now
- 05:0105:01, 27 September 2017 diff hist +2 m Butlin:Unix for Bioinformatics - basic tutorial /* TASK 2: My NGS library has finally been sequenced and my sequencing centre has informed me that the sequence data files are on one of their password protected servers ready for download. How do I get those many Gb large files into my iceberg account...
- 04:1904:19, 27 September 2017 diff hist +14 Butlin:Unix for Bioinformatics - basic tutorial →fixed to file storage on iceberg
- 04:1704:17, 27 September 2017 diff hist −5 m Butlin:Unix for Bioinformatics - basic tutorial →TASK 1: How do I do a local install of a suite of programmes that come as C++ source code?
- 04:0604:06, 27 September 2017 diff hist +48 Butlin:Unix for Bioinformatics - basic tutorial →added ./configure command before make of samtools
- 03:4903:49, 27 September 2017 diff hist +47 Butlin:Unix for Bioinformatics - basic tutorial →fixed wget command
- 03:4703:47, 27 September 2017 diff hist +466 m Butlin:Unix for Bioinformatics - basic tutorial →If you don't have have access to iceberg
- 03:4603:46, 27 September 2017 diff hist −493 Butlin:Unix for Bioinformatics - basic tutorial →changed download link for samtools1.3 to use the sourceforge server
- 03:3703:37, 27 September 2017 diff hist +2 Butlin:Unix for Bioinformatics - basic tutorial →set new link to website that explains permissions
- 03:2803:28, 27 September 2017 diff hist −40 Butlin:Unix for Bioinformatics - basic tutorial →changed long Dropbox link to tiny url
- 03:2403:24, 27 September 2017 diff hist +744 Butlin:Unix for Bioinformatics - basic tutorial →Added Cmd + TAB tip
- 03:1503:15, 27 September 2017 diff hist +47 Butlin:Unix for Bioinformatics - basic tutorial →added new download link to example data, which is now on my private Dropbox
- 02:3402:34, 27 September 2017 diff hist +668 Butlin:Unix for Bioinformatics - basic tutorial →Added troubleshooting ; made minor changes to explanantion ; fixed curly quotes
- 01:3701:37, 27 September 2017 diff hist −5 m Butlin:Unix for Bioinformatics - basic tutorial →Before you jump into this tutorial
- 01:3401:34, 27 September 2017 diff hist +125 m Butlin:Unix for Bioinformatics - basic tutorial →Some basics
- 01:0201:02, 27 September 2017 diff hist +179 m Butlin:Unix for Bioinformatics - basic tutorial →Before you jump into this tutorial
- 00:4800:48, 27 September 2017 diff hist +77 m Butlin:Unix for Bioinformatics - basic tutorial →Before you jump into this tutorial
26 September 2017
- 14:1214:12, 26 September 2017 diff hist −183 m Talk:Butlin:Unix for Bioinformatics - advanced tutorial No edit summary current
- 14:1014:10, 26 September 2017 diff hist −158 m Butlin:Unix for Bioinformatics - advanced tutorial /* TASK 12: I need to run programme X that requires 2 input files and cannot read compressed files. My input files are very large and disk space is always precious. How can I avoid first having to uncompress my input files and later recompress them whe...
- 14:1014:10, 26 September 2017 diff hist +804 Butlin:Unix for Bioinformatics - advanced tutorial →Added blurb to endnote, with link to Arnie's speech
- 13:4913:49, 26 September 2017 diff hist +2 m Butlin:Unix for Bioinformatics - advanced tutorial →Notes
- 13:4413:44, 26 September 2017 diff hist 0 Butlin:Unix for Bioinformatics - basic tutorial →put definition of Unix to the front
- 13:4013:40, 26 September 2017 diff hist +961 Butlin:Unix for Bioinformatics - basic tutorial →Added appeal not to copy-paste command lines
- 04:0604:06, 26 September 2017 diff hist +148 Butlin:Unix for Bioinformatics - advanced tutorial →Added troublehooting tip: when rename.pl download link does not work, go to my Dropbox
- 02:4402:44, 26 September 2017 diff hist +168 Butlin:Unix for Bioinformatics - advanced tutorial →added Troubleshooting tip
- 02:3602:36, 26 September 2017 diff hist +18 m Butlin:Unix for Bioinformatics - advanced tutorial →TASK 5: I have split my reads by barcode and I have quality filtered them. Now I want to know how many reads I have left from each (barcoded) individual. How can I find that out?
19 September 2017
- 09:4209:42, 19 September 2017 diff hist +5 Butlin:Unix for Bioinformatics - advanced tutorial /* TASK 12: I need to run programme X that requires 2 input files and cannot read compressed files. My input files are very large and disk space is always precious. How can I avoid first having to uncompress my input files and later recompress them w
- 09:4109:41, 19 September 2017 diff hist 0 Butlin:Unix for Bioinformatics - advanced tutorial →TASK 9: I have got a big multi-fasta file with thousands of sequences. How can I extract only those fasta records whose sequences contain at least 3 consecutive repeats of the dinucleotide AG?
- 09:1309:13, 19 September 2017 diff hist −2 Butlin:Unix for Bioinformatics - advanced tutorial /* TASK 10: I have a large table from the output of the programme stacks containing the condensed information for each reference tag. Each column is tab delimited. The first column contains the tag ids. Another column the reference sequence for the t
- 08:5908:59, 19 September 2017 diff hist −4 Butlin:Unix for Bioinformatics - advanced tutorial →TASK 9: I have got a big multi-fasta file with thousands of sequences. How can I extract only those fasta records whose sequences contain at least 3 consecutive repeats of the dinucleotide AG?
- 08:5508:55, 19 September 2017 diff hist −2 Butlin:Unix for Bioinformatics - advanced tutorial →TASK 9: I have got a big multi-fasta file with thousands of sequences. How can I extract only those fasta records whose sequences contain at least 3 consecutive repeats of the dinucleotide AG?
- 08:5408:54, 19 September 2017 diff hist −4 Butlin:Unix for Bioinformatics - advanced tutorial →TASK 9: I have got a big multi-fasta file with thousands of sequences. How can I extract only those fasta records whose sequences contain at least 3 consecutive repeats of the dinucleotide AG?
- 08:5308:53, 19 September 2017 diff hist −2 Butlin:Unix for Bioinformatics - advanced tutorial →TASK 9: I have got a big multi-fasta file with thousands of sequences. How can I extract only those fasta records whose sequences contain at least 3 consecutive repeats of the dinucleotide AG?
14 September 2017
- 08:5808:58, 14 September 2017 diff hist +8 Butlin:Unix for Bioinformatics - advanced tutorial /* TASK 11: I want to map the reads from 96 individuals against a reference sequence (e. g. partial or full reference genome or transcriptome, etc.). A mapping programme takes one of the 96 input files and tries to find locations for each read in the
- 08:5608:56, 14 September 2017 diff hist +21 Butlin:Unix for Bioinformatics - advanced tutorial →If you are working on a multi core machine
- 08:4108:41, 14 September 2017 diff hist +3 Butlin:Unix for Bioinformatics - advanced tutorial /* TASK 12: I need to run programme X that requires 2 input files and cannot read compressed files. My input files are very large and disk space always precious. How can I avoid first having to uncompress my input files and later recompress them when
- 08:4008:40, 14 September 2017 diff hist +55 Butlin:Unix for Bioinformatics - advanced tutorial /* TASK 12: I need to run programme X that requires 2 input files and cannot read compressed files. My input files are very large and disk space always precious. How can I avoid first having to uncompress my input files and later recompress them when
- 08:3808:38, 14 September 2017 diff hist −125 Butlin:Unix for Bioinformatics - advanced tutorial /* TASK 12: I need to run programme X that requires 2 input files and cannot read compressed files. My input files are very large and disk space always precious. How can I avoid first having to uncompress my input files and later recompress them when