Hello,
I'm new to the bioinformatics side of life and started to use ABySS for allignement. I have however an input file which is not in FASTA format.
For example the lines look like:
@HWI-EAS313_0005:1:1:1158:9100#0/1
TCGATAGGCCGTGGACAGNGCTGACCGTAGGGGTGGGCTGNGNNNNNNTANGTACGTGNCTGGGTGTACCGAATANNCNT
+HWI-EAS313_0005:1:1:1158:9100#0/1
cbdddccddcece^c_ZbBb``b``cdddddcdad[`Vb^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
with in the second line the sequence and in the fouth line the quality score.
I wondered whether there is a command line with which ABySS could read this file (and therefore include the quality scores in the analysis as they are quite important) or whether it is easier to make a FASTA file from this txt file. In the latter case does anyone knows a quick way to do that?
Tanks
I'm new to the bioinformatics side of life and started to use ABySS for allignement. I have however an input file which is not in FASTA format.
For example the lines look like:
@HWI-EAS313_0005:1:1:1158:9100#0/1
TCGATAGGCCGTGGACAGNGCTGACCGTAGGGGTGGGCTGNGNNNNNNTANGTACGTGNCTGGGTGTACCGAATANNCNT
+HWI-EAS313_0005:1:1:1158:9100#0/1
cbdddccddcece^c_ZbBb``b``cdddddcdad[`Vb^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
with in the second line the sequence and in the fouth line the quality score.
I wondered whether there is a command line with which ABySS could read this file (and therefore include the quality scores in the analysis as they are quite important) or whether it is easier to make a FASTA file from this txt file. In the latter case does anyone knows a quick way to do that?
Tanks
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