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2 hours ago by

**I am begining with bioinformatic genomic. I am very intereted in NIPT. I use SeqFF.R package for estimating fetal fraction. I downloaded seqff.R package in obgyn.onlinelibrary.wiley.com/doi/abs/10.1002/pd.4615. I have file seqFF.R, SupplementalTable1.cvs, SupplementalTable2.cvs and file Supplemental.Rdata.

**I have some fastq files generated by BGI machine. I used bowtie2 for convert fastq file to sam file. Then, I used picard tool for sam file to sorted.sam

**And, sorted.sam >noheadersam with command: grep -v '^@' sorted.sam > noheader.sam

**The last, I use 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: Rscript seqff.r --i /home/tools/ --f noheader.sam --d /home/tools/ --o result --t sam

** Rscript run error setwd(input.dir). I don't solve it. I'd be thankful if somebody helps me with this, specialy detailing



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