Hi all,
I need some help on fastx-toolkit use.
I would like to generate nucleotide distribution line graph but I don't manage.
Below is command lines that I used :
1-to obtain statistics report
cat ../../sequences/phix/s_4_1_sequence.txt | fastx_quality_stats -o ../../sequences/phix/s_4_1_qual_stat.txt
2-to create distribution graph
fastx_nucleotide_distribution_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_s_4_1.png
that worked.
3-to create distribution line graph
fastx_nucleotide_distribution_line_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_line_s_4_1.png
It returned:
Error: Input file is not a valid statistics report.
This tool (fastq-quality-plot) requires a tabular text file conaining summary statistic about your FASTQ file.
In Galaxy,
Please use the "Compute Quality Statistics" tool (in the "NGS: QC and Manipulation" category) to compute the quality statistics report, and then use this tool with the new statistics report.
On the command line,
Please use the "fastx_quality_stats" program to create the statistics report.
I thought both distribution scripts work similary and have only different output graphs. Maybe I am wrong.
Why does it work in one case and not in the other with same statistics report file as input ?
Thanks for help.
Jennifer
I need some help on fastx-toolkit use.
I would like to generate nucleotide distribution line graph but I don't manage.
Below is command lines that I used :
1-to obtain statistics report
cat ../../sequences/phix/s_4_1_sequence.txt | fastx_quality_stats -o ../../sequences/phix/s_4_1_qual_stat.txt
2-to create distribution graph
fastx_nucleotide_distribution_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_s_4_1.png
that worked.
3-to create distribution line graph
fastx_nucleotide_distribution_line_graph.sh -i ../../../sequences/phix/s_4_1_qual_stat.txt -o ../../../sequences/phix/nuc_distri_line_s_4_1.png
It returned:
Error: Input file is not a valid statistics report.
This tool (fastq-quality-plot) requires a tabular text file conaining summary statistic about your FASTQ file.
In Galaxy,
Please use the "Compute Quality Statistics" tool (in the "NGS: QC and Manipulation" category) to compute the quality statistics report, and then use this tool with the new statistics report.
On the command line,
Please use the "fastx_quality_stats" program to create the statistics report.
I thought both distribution scripts work similary and have only different output graphs. Maybe I am wrong.
Why does it work in one case and not in the other with same statistics report file as input ?
Thanks for help.
Jennifer
Comment