How to use seqff.r script (estimating fetal fraction)

Question

[Lucas]

Hi Dear Colleagues,

I downloaded seqff package here, but I don't know how to use it properly. I have some fastq files generated by Illumina machine, I want to analyze them, as I understood, I have to convert them to mapped sam files and then analyze them using seqff.r script.

The seqff.r script accepts some arguments as follow:

--i input directory

--f input file name

--d output directory

--o output file name

--t data type; sam file (without header) or tabulated read counts ordered by genomic coordinates found in SupplementalTable1.csv

I'm using the command as follow, but it fails:

Rscript seqff.r --i /home/lucas/seqff/ --f NIPT001.sam --d /home/lucas/seqff/ --o result --t sam

Am I using the options correctly? I created the mapped sam file from fastq file using bwa and then removed the headers using the below command:

grep -v '^@' file.sam > noheader.sam

But the seqff.r script fails, I'd be thankful if somebody helps me with this.

[son.hmu0915]

hi. Your problem fixed how? I want to use it,

[son.hmu0915]

I use machine BGI and, file sequencing Fatq. I want to analyze them.I'd be thankful if somebody helps me with pipepline use it.

[GenoMax]

Please don't post answers in threads with your own questions. Have you familiarized yourself with background on next generation sequencing data? There is no single monolithic pipeline to "analyze fastq" files. What kind of an experiment is this?

[smrutimayipanda]

Hii @khanhlpbao, Can you please tell me how did your script worked? Actually I am getting the same error, due to different directories and filenames, the script is not working at all.

[khanhlpbao]

Hi @smrutimayipanda, in lines 35-39, I replace the " " into "=" like this

input.dir = unlist(strsplit(arg[ pmatch("--i",arg)], "="))[2]
file.name = unlist(strsplit(arg[ pmatch("--f",arg)], "="))[2]
output.dir = unlist(strsplit(arg[ pmatch("--d",arg)], "="))[2]
output.filename = unlist(strsplit(arg[ pmatch("--o",arg)], "="))[2]
datatype = unlist(strsplit(arg[ pmatch("--t",arg)], "="))[2]

Then when turn on the script, I type

--i=/path/to/input/folder --f=sample.sam --d=/path/to/output/folder --o=ff.txt --t=sam

You can choose .sam file automatically by type datatype = "sam" instead of the command to recognize it on args. Hope it can help you

[smrutimayipanda]

It is already there in script. There is no need of replacing.

[smrutimayipanda]

I tried your suggestions but didnt get any result. Did you use this script on your own? Can you tell me about inputs?

Answer 1

[khanhlpbao]

Hi I just beginning in bioinformatics, but I hope that my answer can help you I have the error in input.dir, turns out the R code for extract directories and filenames cannot work on R 4.0 (the version I'm using). Now I have to add my directory and filenames to it by my hand and its worked. But the working is not fully 100%, SeqFF and Enet returned with NA, only WRSC returned with result.

[vasanthmandla]

Dear @khanhlpbao,

Do you know what does the "FRS" mean in the "supplementary-table2.csv" file.

Thanks in advance

[vasanthmandla]

Got the answer "fetal ratio statistic". But, could some one help me in understanding how it is calculated.