Hi,
I am new to NGS data analysis and I have got some ELAND output files (specificially the sorted.txt file) which I am planning to analyse using MACS. However, MACS keeps falling over due to a "Strand information can not be recognized in this line" error. I have deduced that this is due to a backspace characters which have appeared between some characters in my file and because MACS can't find a tab between the characters it complains that the line is not in the correct format.
Here is the offending line: (see the '^H' between the 0 and 1)
HWI-EAS486 23 1 97 11471 15019 0^H1 CAGGGTCACCCAGAGTGAGTGTGAAGCCAGCCTGAGATC hhYghhhhhhhggfhhghhhgghghghhhghghhhdfch chr10.fa 80424503 F 34G1C1A 6
Here is the same line as output by the MACS error: (backspace represented as x08 (HEX I think)
HWI-EAS486\t23\t1\t97\t11471\t15019\t0\x081\tCAGGGTCACCCAGAGTGAGTGTGAAGCCAGCCTGAGATC\thhYghhhhhhhggfhhghhhgghghghhhghghhhdfch\tchr10.fa\t\t80424503\tF\t34G1C1A\t6","34G1C1A
Does anyone have any idea how to replace these ^H (x08) backspace characters with tabs? the problem I have is that there are numerous occurances of ^H in the file which are legitimate.
Any help of advice would be very useful.
Thanks
I am new to NGS data analysis and I have got some ELAND output files (specificially the sorted.txt file) which I am planning to analyse using MACS. However, MACS keeps falling over due to a "Strand information can not be recognized in this line" error. I have deduced that this is due to a backspace characters which have appeared between some characters in my file and because MACS can't find a tab between the characters it complains that the line is not in the correct format.
Here is the offending line: (see the '^H' between the 0 and 1)
HWI-EAS486 23 1 97 11471 15019 0^H1 CAGGGTCACCCAGAGTGAGTGTGAAGCCAGCCTGAGATC hhYghhhhhhhggfhhghhhgghghghhhghghhhdfch chr10.fa 80424503 F 34G1C1A 6
Here is the same line as output by the MACS error: (backspace represented as x08 (HEX I think)
HWI-EAS486\t23\t1\t97\t11471\t15019\t0\x081\tCAGGGTCACCCAGAGTGAGTGTGAAGCCAGCCTGAGATC\thhYghhhhhhhggfhhghhhgghghghhhghghhhdfch\tchr10.fa\t\t80424503\tF\t34G1C1A\t6","34G1C1A
Does anyone have any idea how to replace these ^H (x08) backspace characters with tabs? the problem I have is that there are numerous occurances of ^H in the file which are legitimate.
Any help of advice would be very useful.
Thanks
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