Last updated: 2020-02-19
Checks: 7 0
Knit directory: misc/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 460fe4b | Dongyue Xie | 2020-02-19 | wflow_publish(“analysis/GTEX.Rmd”) |
| html | b85c283 | Dongyue Xie | 2020-01-15 | Build site. |
| Rmd | 605578a | Dongyue Xie | 2020-01-15 | wflow_publish(“analysis/GTEX.Rmd”) |
Number of SRA RNA seq files:
Heart - 369
Brain - 1055
Lung - 242
Muscle - 330
Nerve - 238
Thyroid - 250
for i in {SRR1069802,SRR1071692,SRR1072650,SRR1075631,SRR1075997,SRR1076779,SRR1077115,SRR1077528,SRR1077643};
do
prefetch $i;
rm *.1;
rm *.10;
rm *.11;
rm *.9;
rm *.13;
rm *.8;
doneAn easier one(could try later):
cat your_accession_list.txt | while read i
do
fasterq-dump ${i} <options>
donetry for loop…too slow
for i in {SRR1069690,SRR1069802,SRR1071692,SRR1072650,SRR1075631,SRR1075997,SRR1076779,SRR1077115,SRR1077528,SRR1077643};
do
sam-dump $i.sra | samtools view -Sb > /project2/mstephens/dongyue/gtex/$i.bam ;
done
try the parallel version
find *.sra | parallel 'sam-dump {} | samtools view -Sb > /project2/mstephens/dongyue/gtex/{/.}.bam'
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.5.0 Rcpp_1.0.2 rprojroot_1.3-2 digest_0.6.21
[5] later_1.0.0 R6_2.4.0 backports_1.1.5 git2r_0.26.1
[9] magrittr_1.5 evaluate_0.14 stringi_1.4.3 rlang_0.4.0
[13] fs_1.3.1 promises_1.1.0 whisker_0.4 rmarkdown_1.16
[17] tools_3.6.1 stringr_1.4.0 glue_1.3.1 httpuv_1.5.2
[21] xfun_0.10 yaml_2.2.0 compiler_3.6.1 htmltools_0.4.0
[25] knitr_1.25