fastq file data

Question

[Sam]

Hello

how I can show nucleotide distribution and sequence length of multi fastq file (1.fq, 2.fq,...,6.fq) in just 2 separate graph?

Thanks

[Pierre Lindenbaum]

what have you tried/found so far ?

[Sam]

fastx-tool kit but it just for one lib and I want merge all lib data in one geraph

[Pierre Lindenbaum]

what about merging the fastq files before running fastx ?

[Sam]

I don't want merge all reads , just want show sequence length of multi fq file , separately (for instance according color ) in one graph

[Pierre Lindenbaum]

I don't want merge all reads

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

"Tools can read from STDIN "

I think you should consider this option.

[Sam]

should use output of fastx_quality_stats , as input for FASTA/Q Nucleotide Distribution

, so is it a right command ?

fastx_nucleotide_distribution_graph.sh -i file1.TXT file2.TXT file3.TXT [-t TITLE]  [-o OUTPUT]

[GenoMax]

No harm is trying the command out :)

[Pierre Lindenbaum]

I think it should be something like

gunzip -c *.fq.gz | fastx_nucleotide_distribution_graph.sh - o OUTPUT

[WouterDeCoster]

This is probably about Illumina data, but it never hurts to mention this!

[Sam]

above commands not work , except hurts and harm topic fast reply! could you help to find a way ?

[WouterDeCoster]

You didn't tell us where you got the data from. So, Illumina data?

above commands not work

You'll have to tell us a bit more about how those don't work.

[Pierre Lindenbaum]

above commands not work

[Sam]

but I explained all story, fastx_nucleotide_distribution_graph.sh just take TXT out put file of fastx_quality_stats as input, with one txt input file fastx_nucleotide_distribution_graph.sh works well but with two input file( -i file1.txt file2.txt) I got this error:

gnuplot> set term png size 1048,768
                  ^
         line 0: unknown or ambiguous terminal type; type just 'set terminal' for a list

WARNING: Plotting with an 'unknown' terminal.

It's illumina fq files, could you introduce other scripts ?

[WouterDeCoster]

Anything wrong with FastQC?

[Sam]

no all thing is OK with FASTQC , I can post only 5 post per 6hr, is there any way to improve it ?

[WouterDeCoster]

I can post only 5 post per 6hr, is there any way to improve it ?

After you have been on Biostars for a while this restriction will be removed.

[Pierre Lindenbaum]

fastx calls gnuplot ; it seems that your version is not complete:

https://stackoverflow.com/questions/22816030

[Sam]

it's works without any problem with -i file1.text , and I have a nice plot in out put , problem is fastx_nucleotide_distribution_graph.sh is not compatible with more than one input file. so I should find other alternative scripts for merge nucleotide_distribution_graph from distinct fq file.

[GenoMax]

If you need just one plot for the entire dataset then cat'ing the fastq files together to generate one inout (per read, R1/R2) may be the way to go.

[Sam]

I think to a awk code to have a sequence length frequency in each fq file and then merge them in Excel to have a unique sequence length graph with different color for each lib.

Answer 1

[Istvan Albert]

FastQC produces both plots.