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  • Converting GEO database TXT format to fasta

    Hello!

    I'm new to bioinformatics, but I need to perform an analysis of some sort.

    I've downloaded data from GEO database it's a large TXT file consisting of many lines that look this way : SCS_0004:2:1:1053:18066#0/1 AGCAATATTGACTACANCCTCATCAAAGCCTGTAGGCACC [YITQR]MST\WN\\TEQU[`]WU]]WPYXXXOXU]`\W` 5 29 29 chr17:68048647-68172163_36129 3979 + 1 1

    I need to align those short sequences to a mouse chromosome, and I'm using bowtie under windows.

    But the problem is , bowtie doesn't work with this format, can you recommend an easy-to-use tool for windows to convert this format into fasta or just raw?

  • #2
    This could be done with the unix command line but it would be helpful if you can post a few lines enclosed within code brackets like
    Code:
    paste here
    to get a precise idea of the file format.

    Comment


    • #3
      Originally posted by vivek_ View Post
      This could be done with the unix command line but it would be helpful if you can post a few lines enclosed within code brackets like
      Code:
      paste here
      to get a precise idea of the file format.
      Code:
      SCS_0004:2:1:1053:18066#0/1	AGCAATATTGACTACANCCTCATCAAAGCCTGTAGGCACC	[YITQR]MST\WN\\TEQU[`]WU]]WPYXXXOXU]`\W`	5	29	29	chr17:68048647-68172163_36129	3979	+	1	1
      SCS_0004:2:1:1053:18066#0/1	AGCAATATTGACTACANCCTCATCAAAGCCTGTAGGCACC	[YITQR]MST\WN\\TEQU[`]WU]]WPYXXXOXU]`\W`	5	29	29	chr17:68048647-68172163_36130	3979	+	1	1
      SCS_0004:2:1:1053:18066#0/1	AGCAATATTGACTACANCCTCATCAAAGCCTGTAGGCACC	[YITQR]MST\WN\\TEQU[`]WU]]WPYXXXOXU]`\W`	5	29	29	uc008dkh.1	4033	+	1	1
      SCS_0004:2:1:1053:18066#0/1	AGCAATATTGACTACANCCTCATCAAAGCCTGTAGGCACC	[YITQR]MST\WN\\TEQU[`]WU]]WPYXXXOXU]`\W`	5	29	29	chr17:68046720-68172163_36128	3943	+	1	1
      SCS_0004:2:1:1053:18066#0/1	AGCAATATTGACTACANCCTCATCAAAGCCTGTAGGCACC	[YITQR]MST\WN\\TEQU[`]WU]]WPYXXXOXU]`\W`	5	29	29	chr17:68046720-68172163_36127	3943	+	1	1
      SCS_0004:2:1:1054:5070#0/1	TTTCTCTGTCTTGTCCNCCTAGTTTCCCTCCTGTAGGCAC	aaaaaaaaaaaaaaa]EaaaW]]]Yaa\a`[aa]Pa^]VT	2	30	30	chr2:40378133-40378584_42654	395	-	1	1
      SCS_0004:2:1:1054:5070#0/1	TTTCTCTGTCTTGTCCNCCTAGTTTCCCTCCTGTAGGCAC	aaaaaaaaaaaaaaa]EaaaW]]]Yaa\a`[aa]Pa^]VT	2	30	30	chr1:8926487-8927380_99	16	+	1	1
      Something like this. By the way, I don't have unix installed only Mac OS and windows, but as far as I understand Mac OS is a unix-based system, right?
      Last edited by Etherella; 08-30-2012, 03:03 AM.

      Comment


      • #4
        The easiest way would be to write a small script (in python, perl, whatever) to read that in and spit out the same data (sans alignment information) in fastq format. Column 1 is the read id, column 2 is the sequence, and column 3 is the quality score. If you have python installed on your Mac, then the following would probably work (changing INPUT_FILENAME to the name of the file you got from GEO and SOME_OUTPUT_FILE to whatever you want the output to be):
        Code:
        #!/usr/bin/python
        import csv
        
        f = csv.reader(open("INPUT_FILENAME", "r"), dialect="excel-tab")
        output = open("SOME_OUTPUT_FILE", "w")
        
        last = ""
        for line in f :
            if(line[0] != last) :
                output.write(">%s\n" % (line[0]))
                output.write("%s\n" % (line[1]))
                output.write("+\n") 
                output.write("%s\n" % (line[2]))
                last = line[0]
        output.close()
        Something like that would probably work.

        Comment


        • #5
          thanks for the reply, I managed to get it working through galaxy.

          Comment

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