Closed AnaBVA closed 6 years ago
lcolladotor
commented
6 years ago Thanks for the report @AnaBVA!
@nellore I don't see those 2 samples in https://github.com/nellore/runs/blob/master/sra/v2/hg38/NOTES and indeed https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=SRP041538 shows all 189 samples. Maybe 2 of them were not human RNA-seq? Doesn't seem like it from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1376161 plus it was last updated on Feb 20, 2015.
lcolladotor
commented
6 years ago Hi again @AnaBVA,
Someone else posted a similar question at https://support.bioconductor.org/p/107026/#107038
Running this code:
library('recount')
metadata <- all_metadata()
m <- subset(metadata, project == 'SRP000941')
download_study("SRP000941", type = "rse-gene")
load(file.path("SRP000941", "rse_gene.Rdata"))
m$run[!m$run %in% rse_gene$run]
m[which(!m$run %in% rse_gene$run), ]
download_study("SRP041538", type = "rse-gene")
load(file.path("SRP041538", "rse_gene.Rdata"))
m2 <- subset(metadata, project == 'SRP041538')
m2[which(!m2$run %in% rse_gene$run),]
dim(m2)
leads to
> m2[which(!m2$run %in% rse_gene$run),]
DataFrame with 2 rows and 21 columns
project sample experiment run read_count_as_reported_by_sra reads_downloaded
<character> <character> <character> <character> <integer> <integer>
1 SRP041538 SRS598756 SRX529059 SRR1265670 21072099 0
2 SRP041538 SRS598759 SRX529062 SRR1265673 24673418 0
proportion_of_reads_reported_by_sra_downloaded paired_end sra_misreported_paired_end mapped_read_count
<numeric> <logical> <logical> <integer>
1 0 FALSE FALSE 0
2 0 FALSE FALSE 0
auc sharq_beta_tissue sharq_beta_cell_type biosample_submission_date biosample_publication_date
<numeric> <character> <character> <character> <character>
1 NA NA NA 2014-04-29T13:18:45.987 2015-02-21T01:13:21.747
2 NA NA NA 2014-04-29T13:18:59.670 2015-02-21T01:13:00.620
biosample_update_date avg_read_length geo_accession bigwig_file title
<character> <integer> <character> <character> <character>
1 2015-02-21T02:25:35.350 172 GSM1376161 NA COPD lung tissue 5103-COPD
2 2015-02-21T02:25:25.113 170 GSM1376164 NA COPD lung tissue 565-COPD
characteristics
<CharacterList>
1 disease state: COPD,tissue: lung
2 disease state: COPD,tissue: lungwhich had 0 reads downloaded. @nellore might know why, but in any case, we don't have the files to try to add them to recount2 at this point in time.
Best, Leonardo
> options(width = 120)
> devtools::session_info()
Session info ----------------------------------------------------------------------------------------------------------
setting value
version R version 3.4.3 (2017-11-30)
system x86_64, darwin15.6.0
ui AQUA
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2018-03-16
Packages --------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.4.0)
AnnotationDbi 1.40.0 2017-10-31 Bioconductor
assertthat 0.2.0 2017-04-11 CRAN (R 3.4.0)
backports 1.1.2 2017-12-13 CRAN (R 3.4.3)
base * 3.4.3 2017-12-07 local
base64enc 0.1-3 2015-07-28 CRAN (R 3.4.0)
bindr 0.1 2016-11-13 CRAN (R 3.4.0)
bindrcpp 0.2 2017-06-17 CRAN (R 3.4.0)
Biobase * 2.38.0 2017-10-31 Bioconductor
BiocGenerics * 0.24.0 2017-10-31 Bioconductor
BiocParallel 1.12.0 2017-10-31 Bioconductor
biomaRt 2.34.2 2018-01-20 Bioconductor
Biostrings 2.46.0 2017-10-31 Bioconductor
bit 1.1-12 2014-04-09 CRAN (R 3.4.0)
bit64 0.9-7 2017-05-08 CRAN (R 3.4.0)
bitops 1.0-6 2013-08-17 CRAN (R 3.4.0)
blob 1.1.0 2017-06-17 CRAN (R 3.4.0)
BSgenome 1.46.0 2017-10-31 Bioconductor
bumphunter 1.20.0 2017-10-31 Bioconductor
checkmate 1.8.5 2017-10-24 CRAN (R 3.4.2)
cluster 2.0.6 2017-03-10 CRAN (R 3.4.3)
codetools 0.2-15 2016-10-05 CRAN (R 3.4.3)
colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
compiler 3.4.3 2017-12-07 local
data.table 1.10.4-3 2017-10-27 CRAN (R 3.4.2)
datasets * 3.4.3 2017-12-07 local
DBI 0.8 2018-03-02 CRAN (R 3.4.3)
DelayedArray * 0.4.1 2017-11-07 Bioconductor
derfinder 1.12.6 2018-01-21 Bioconductor
derfinderHelper 1.12.0 2017-10-31 Bioconductor
devtools 1.13.5 2018-02-18 CRAN (R 3.4.3)
digest 0.6.15 2018-01-28 CRAN (R 3.4.3)
doRNG 1.6.6 2017-04-10 CRAN (R 3.4.0)
downloader 0.4 2015-07-09 CRAN (R 3.4.0)
dplyr 0.7.4 2017-09-28 CRAN (R 3.4.2)
foreach 1.4.4 2017-12-12 CRAN (R 3.4.3)
foreign 0.8-69 2017-06-22 CRAN (R 3.4.3)
Formula 1.2-2 2017-07-10 CRAN (R 3.4.1)
GenomeInfoDb * 1.14.0 2017-10-31 Bioconductor
GenomeInfoDbData 1.0.0 2018-01-09 Bioconductor
GenomicAlignments 1.14.1 2017-11-18 Bioconductor
GenomicFeatures 1.30.3 2018-02-02 Bioconductor
GenomicFiles 1.14.0 2017-10-31 Bioconductor
GenomicRanges * 1.30.3 2018-02-26 Bioconductor
GEOquery 2.46.15 2018-03-02 Bioconductor
ggplot2 2.2.1 2016-12-30 CRAN (R 3.4.0)
glue 1.2.0 2017-10-29 CRAN (R 3.4.2)
graphics * 3.4.3 2017-12-07 local
grDevices * 3.4.3 2017-12-07 local
grid 3.4.3 2017-12-07 local
gridExtra 2.3 2017-09-09 CRAN (R 3.4.1)
gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)
Hmisc 4.1-1 2018-01-03 CRAN (R 3.4.3)
hms 0.4.1 2018-01-24 CRAN (R 3.4.3)
htmlTable 1.11.2 2018-01-20 CRAN (R 3.4.3)
htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0)
htmlwidgets 1.0 2018-01-20 CRAN (R 3.4.3)
httr 1.3.1 2017-08-20 CRAN (R 3.4.1)
IRanges * 2.12.0 2017-10-31 Bioconductor
iterators 1.0.9 2017-12-12 CRAN (R 3.4.3)
jsonlite 1.5 2017-06-01 CRAN (R 3.4.0)
knitr 1.20 2018-02-20 cran (@1.20)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.3)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.4.0)
lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.2)
limma 3.34.9 2018-02-22 Bioconductor
locfit 1.5-9.1 2013-04-20 CRAN (R 3.4.0)
magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
Matrix 1.2-12 2017-11-20 CRAN (R 3.4.3)
matrixStats * 0.53.1 2018-02-11 CRAN (R 3.4.3)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
methods * 3.4.3 2017-12-07 local
munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.4.3)
parallel * 3.4.3 2017-12-07 local
pillar 1.2.1 2018-02-27 CRAN (R 3.4.3)
pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.0)
pkgmaker 0.22 2014-05-14 CRAN (R 3.4.0)
plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.0)
progress 1.1.2 2016-12-14 CRAN (R 3.4.0)
purrr 0.2.4 2017-10-18 CRAN (R 3.4.2)
qvalue 2.10.0 2017-10-31 Bioconductor
R6 2.2.2 2017-06-17 CRAN (R 3.4.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.4.0)
Rcpp 0.12.15 2018-01-20 CRAN (R 3.4.3)
RCurl 1.95-4.10 2018-01-04 CRAN (R 3.4.3)
readr 1.1.1 2017-05-16 CRAN (R 3.4.0)
recount * 1.4.5 2018-03-01 Bioconductor
registry 0.5 2017-12-03 CRAN (R 3.4.3)
rentrez 1.2.1 2018-03-05 CRAN (R 3.4.3)
reshape2 1.4.3 2017-12-11 CRAN (R 3.4.3)
rlang 0.2.0 2018-02-20 CRAN (R 3.4.3)
RMySQL 0.10.14 2018-02-26 CRAN (R 3.4.3)
rngtools 1.2.4 2014-03-06 CRAN (R 3.4.0)
rpart 4.1-13 2018-02-23 CRAN (R 3.4.3)
Rsamtools 1.30.0 2017-10-31 Bioconductor
RSQLite 2.0 2017-06-19 CRAN (R 3.4.1)
rstudioapi 0.7 2017-09-07 CRAN (R 3.4.1)
rtracklayer 1.38.3 2018-01-23 Bioconductor
S4Vectors * 0.16.0 2017-10-31 Bioconductor
scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
splines 3.4.3 2017-12-07 local
stats * 3.4.3 2017-12-07 local
stats4 * 3.4.3 2017-12-07 local
stringi 1.1.6 2017-11-17 CRAN (R 3.4.2)
stringr 1.3.0 2018-02-19 cran (@1.3.0)
SummarizedExperiment * 1.8.1 2017-12-19 Bioconductor
survival 2.41-3 2017-04-04 CRAN (R 3.4.3)
tibble 1.4.2 2018-01-22 CRAN (R 3.4.3)
tidyr 0.8.0 2018-01-29 CRAN (R 3.4.3)
tools 3.4.3 2017-12-07 local
utils * 3.4.3 2017-12-07 local
VariantAnnotation 1.24.5 2018-01-06 Bioconductor
withr 2.1.1 2017-12-19 CRAN (R 3.4.3)
XML 3.98-1.10 2018-02-19 CRAN (R 3.4.3)
xml2 1.2.0 2018-01-24 CRAN (R 3.4.3)
xtable 1.8-2 2016-02-05 CRAN (R 3.4.0)
XVector 0.18.0 2017-10-31 Bioconductor
zlibbioc 1.24.0 2017-10-31 Bioconductor List all samples with this issue (for future reference):
> length(which(metadata$reads_downloaded == 0))
[1] 420
> which(metadata$reads_downloaded == 0)
[1] 49673 49674 49675 49676 49677 49678 49679 49680 49681 49682 49683 49684 49685 49687 49688 49689 49690 49691 49692 49693 49694 49695 49696
[24] 49697 49698 49699 49700 49701 49702 49703 49704 49705 49706 49707 49708 49709 49710 49711 49712 49713 49714 49715 49716 49717 49718 49719
[47] 49720 49721 49722 49723 49724 49725 49726 49727 49728 49729 49730 49731 49732 49733 49734 49735 49736 49737 49738 49739 49740 49741 49742
[70] 49743 49744 49745 49746 49747 49748 49749 49750 49751 49752 49753 49754 49755 49756 49757 49758 49759 49760 49761 49762 49763 49764 49765
[93] 49766 49767 49768 49769 49770 49771 49774 49778 49779 49781 49782 49783 49784 49785 49786 49787 49788 49789 49790 49791 49792 49793 49794
[116] 49795 49796 49797 49798 49799 49800 49801 49802 49803 49804 49805 49806 49807 49808 49809 49810 49811 49812 49813 49814 49815 49816 49817
[139] 49818 49819 49820 49821 49822 49823 49824 49825 49826 49827 49828 49829 49830 49831 49832 49833 49834 49835 49836 49837 49838 49839 49840
[162] 49841 49842 49843 49844 49845 49846 49847 49848 49849 49850 49851 49852 49853 49854 49855 49856 49857 49858 49859 49860 49861 49862 49863
[185] 49864 49865 49866 49867 49868 49869 49870 49871 49872 49873 49874 49875 49876 49877 49878 49879 49880 49881 49882 49883 49884 49885 49886
[208] 49887 49888 49889 49890 49891 49892 49893 49894 49895 49896 49897 49898 49899 49900 49901 49902 49903 49904 49905 49906 49907 49908 49909
[231] 49910 49911 49912 49913 49914 49915 49916 49917 49918 49919 49920 49921 49922 49923 49924 49925 49926 49927 49928 49929 49930 49931 49932
[254] 49933 49934 49935 49936 49937 49938 49939 49940 49941 49942 49943 49944 49945 49946 49947 49948 49949 49950 49951 49952 49953 49954 49955
[277] 49956 49957 49958 49959 49960 49961 49962 49963 49964 49965 49966 49967 49968 49969 49970 49971 49972 49973 49974 49975 49976 49977 49978
[300] 49979 49980 49981 49982 49983 49984 49985 49986 49987 49988 49989 49990 49991 49992 49993 49994 49995 49996 49997 49998 49999 50000 50001
[323] 50002 50003 50004 50005 50006 50007 50008 50009 50010 50011 50012 50013 50014 50015 50016 50017 50018 50019 50020 50021 50022 50023 50024
[346] 50025 50026 50027 50028 50029 50030 50031 50032 50033 50034 50035 50036 50037 50038 50039 50040 50041 50042 50043 50044 50045 50046 50047
[369] 50048 50049 50050 50051 50052 50053 50054 50055 50056 50057 50058 50059 50060 50061 50062 50063 50064 50065 50066 50067 50068 50069 50070
[392] 50071 50072 50073 50074 50075 50076 50077 50078 50079 50080 50081 50082 50083 50084 50085 50086 50087 50088 50089 50090 50091 50092 50093
[415] 50094 50095 50096 50097 50098 50099
> metadata$run[which(metadata$reads_downloaded == 0)]
[1] "DRR006495" "DRR015319" "DRR023393" "DRR023424" "DRR028205" "DRR028310" "DRR028518" "DRR028367" "DRR028441" "DRR028465"
[11] "DRR024823" "DRR029119" "ERR030883" "ERR313163" "ERR313164" "ERR313181" "ERR313182" "ERR313172" "ERR313175" "ERR184045"
[21] "ERR188322" "ERR188313" "ERR188234" "ERR188427" "ERR210958" "ERR229796" "ERR304490" "ERR315373" "ERR315480" "ERR315496"
[31] "ERR315497" "ERR321982" "ERR321983" "ERR321984" "ERR321985" "ERR321986" "ERR321987" "ERR321988" "ERR321989" "ERR321990"
[41] "ERR321991" "ERR321992" "ERR321993" "ERR321994" "ERR321995" "ERR321996" "ERR321997" "ERR321998" "ERR342877" "ERR455334"
[51] "ERR689574" "ERR502855" "ERR590834" "ERR659415" "ERR659329" "ERR519519" "ERR519504" "ERR519501" "ERR519492" "ERR519508"
[61] "ERR731460" "ERR698050" "ERR571498" "ERR571504" "ERR576279" "ERR946961" "ERR661160" "ERR661167" "ERR661168" "ERR661169"
[71] "ERR661170" "ERR668352" "ERR668404" "ERR862982" "ERR732562" "ERR732564" "ERR732566" "ERR732568" "ERR732569" "ERR732570"
[81] "ERR732571" "ERR732572" "ERR732573" "ERR732580" "ERR732581" "ERR732582" "ERR732583" "ERR752738" "ERR752896" "ERR895727"
[91] "ERR895728" "ERR895729" "ERR895730" "ERR895731" "ERR950171" "ERR952468" "ERR979105" "ERR979106" "ERR979110" "ERR979114"
[101] "ERR979115" "ERR979117" "ERR979118" "ERR1018449" "ERR1018450" "ERR1018445" "ERR1018458" "ERR1018452" "ERR1018448" "ERR1018453"
[111] "ERR1018451" "ERR1018459" "ERR1018454" "ERR1018456" "ERR1018457" "ERR1018455" "ERR1018444" "ERR1018447" "ERR1018443" "ERR1018446"
[121] "ERR1079180" "ERR1079181" "ERR1079182" "ERR1079183" "ERR1079184" "ERR1079185" "ERR1079186" "ERR1103735" "ERR1103736" "ERR1103737"
[131] "ERR1103738" "ERR1103739" "ERR1103740" "ERR1103741" "ERR1103742" "ERR1103743" "ERR1103744" "ERR1103745" "ERR1103746" "SRR1220437"
[141] "SRR1220440" "SRR029126" "SRR453393" "SRR453400" "SRR980470" "SRR031856" "SRR032117" "SRR066462" "SRR527674" "SRR073757"
[151] "SRR627492" "SRR191676" "SRR537103" "SRR537112" "SRR315317" "SRR317058" "SRR317095" "SRR330905" "SRR333658" "SRR333721"
[161] "SRR387406" "SRR393833" "SRR390511" "SRR393766" "SRR397061" "SRR397069" "SRR397009" "SRR397194" "SRR397379" "SRR398216"
[171] "SRR403883" "SRR420190" "SRR423939" "SRR424575" "SRR490999" "SRR504649" "SRR479057" "SRR479070" "SRR496580" "SRR514129"
[181] "SRR531461" "SRR531711" "SRR553476" "SRR574822" "SRR576928" "SRR585577" "SRR633562" "SRR647504" "SRR650199" "SRR653396"
[191] "SRR764979" "SRR765019" "SRR772684" "SRR292243" "SRR805734" "SRR805783" "SRR805827" "SRR830947" "SRR836504" "SRR896699"
[201] "SRR897184" "SRR897449" "SRR897506" "SRR897682" "SRR897713" "SRR898021" "SRR898027" "SRR902979" "SRR903120" "SRR903123"
[211] "SRR903269" "SRR922553" "SRR923922" "SRR934343" "SRR934824" "SRR934855" "SRR934857" "SRR934904" "SRR942165" "SRR942644"
[221] "SRR944027" "SRR944286" "SRR948503" "SRR950085" "SRR951069" "SRR957955" "SRR960467" "SRR976237" "SRR1002090" "SRR1027584"
[231] "SRR1028013" "SRR1177699" "SRR1027991" "SRR1029673" "SRR1031037" "SRR1033155" "SRR1038585" "SRR1039512" "SRR1268172" "SRR1047309"
[241] "SRR1047862" "SRR1055403" "SRR1060779" "SRR1060781" "SRR1061344" "SRR1067944" "SRR1145842" "SRR1146075" "SRR1146251" "SRR1164866"
[251] "SRR1179133" "SRR1186612" "SRR1186925" "SRR1190463" "SRR1192464" "SRR1192498" "SRR1201765" "SRR1205976" "SRR1213821" "SRR1238497"
[261] "SRR1249341" "SRR1265670" "SRR1265673" "SRR1274250" "SRR1274344" "SRR1283007" "SRR1294564" "SRR1296119" "SRR1296127" "SRR1299462"
[271] "SRR1313148" "SRR1363133" "SRR1363150" "SRR1374350" "SRR1424705" "SRR1462401" "SRR1648446" "SRR1513811" "SRR1513813" "SRR1518364"
[281] "SRR1521367" "SRR1522996" "SRR1525257" "SRR1552965" "SRR1555153" "SRR1560843" "SRR1562722" "SRR1567906" "SRR1571327" "SRR1576165"
[291] "SRR1580542" "SRR1582593" "SRR1583693" "SRR1593513" "SRR1602523" "SRR1602542" "SRR1602551" "SRR1608781" "SRR1608813" "SRR1608879"
[301] "SRR1608900" "SRR1609380" "SRR1609389" "SRR1609409" "SRR1609468" "SRR1616907" "SRR1616911" "SRR1633235" "SRR1633283" "SRR1633349"
[311] "SRR1640724" "SRR1643179" "SRR1643244" "SRR1643265" "SRR1643465" "SRR1643476" "SRR1643557" "SRR1648615" "SRR1661765" "SRR1661842"
[321] "SRR2013710" "SRR1696101" "SRR1700269" "SRR1706868" "SRR1725934" "SRR1736492" "SRR1736495" "SRR1736498" "SRR1737419" "SRR1747251"
[331] "SRR1756572" "SRR1768951" "SRR2046449" "SRR1781862" "SRR1785249" "SRR1792708" "SRR1792704" "SRR1792689" "SRR1792678" "SRR1798135"
[341] "SRR1798134" "SRR1798133" "SRR2093853" "SRR1812720" "SRR1818660" "SRR1821558" "SRR1821412" "SRR2019166" "SRR1918519" "SRR1918416"
[351] "SRR1918413" "SRR1918382" "SRR1918259" "SRR1927041" "SRR1946674" "SRR1946665" "SRR1947543" "SRR1947522" "SRR1947593" "SRR1947589"
[361] "SRR1984203" "SRR1950498" "SRR1971628" "SRR1974912" "SRR1974821" "SRR1974802" "SRR1974626" "SRR1974597" "SRR2980095" "SRR1982630"
[371] "SRR1982585" "SRR2000017" "SRR2001141" "SRR2003819" "SRR2045109" "SRR2045041" "SRR2049448" "SRR2049746" "SRR2049642" "SRR2050428"
[381] "SRR2061479" "SRR2064023" "SRR2072573" "SRR2219564" "SRR2087730" "SRR2088169" "SRR2088123" "SRR2095297" "SRR2107339" "SRR2121674"
[391] "SRR2126724" "SRR2130287" "SRR2138035" "SRR2175388" "SRR2305539" "SRR2305530" "SRR2305526" "SRR2305523" "SRR2305510" "SRR2305505"
[401] "SRR2305483" "SRR2305479" "SRR2313091" "SRR2314022" "SRR2316076" "SRR2532351" "SRR2535181" "SRR2537080" "SRR2544805" "SRR2569751"
[411] "SRR2677524" "SRR2967604" "SRR2967466" "SRR2967276" "SRR2970377" "SRR2968925" "SRR3039610" "SRR3039609" "SRR3039606" "SRR3039620"
> sort(table(metadata$project[which(metadata$reads_downloaded == 0)]))
DRP000987 DRP001358 DRP002586 DRP002860 ERP000546 ERP001908 ERP002063 ERP002232 ERP003460 ERP003917 ERP004573 ERP006215 ERP006216 ERP006577
1 1 1 1 1 1 1 1 1 1 1 1 1 1
ERP007111 ERP008967 ERP010889 ERP010930 SRP001313 SRP001540 SRP001558 SRP003611 SRP003754 SRP004637 SRP005279 SRP007584 SRP007825 SRP007946
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP007947 SRP009316 SRP009840 SRP009862 SRP010061 SRP010280 SRP010679 SRP011546 SRP011927 SRP013021 SRP013825 SRP014670 SRP014675 SRP015361
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP015819 SRP015909 SRP016059 SRP017575 SRP017875 SRP018008 SRP018254 SRP019272 SRP020237 SRP020491 SRP021191 SRP022025 SRP026359 SRP026387
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP027358 SRP028155 SRP028190 SRP028291 SRP028301 SRP028530 SRP028705 SRP028814 SRP029262 SRP029367 SRP029889 SRP030401 SRP031620 SRP032476
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP032775 SRP032833 SRP032999 SRP033098 SRP033135 SRP033335 SRP033351 SRP033569 SRP033696 SRP033725 SRP034626 SRP034737 SRP034875 SRP035930
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP035934 SRP035988 SRP036848 SRP039077 SRP039694 SRP039909 SRP040472 SRP040547 SRP040586 SRP041179 SRP041263 SRP041846 SRP042161 SRP042286
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP042620 SRP043085 SRP043364 SRP043593 SRP044174 SRP044391 SRP044668 SRP044708 SRP044854 SRP045570 SRP045663 SRP045859 SRP045999 SRP046271
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP046293 SRP047192 SRP047299 SRP047366 SRP047407 SRP048536 SRP049553 SRP049714 SRP050499 SRP050892 SRP050992 SRP051083 SRP051368 SRP051644
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP051848 SRP052201 SRP052740 SRP052896 SRP052998 SRP053101 SRP055390 SRP055514 SRP056477 SRP056792 SRP056802 SRP057118 SRP057244 SRP057721
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP057758 SRP057852 SRP059035 SRP059057 SRP059431 SRP059531 SRP059732 SRP060284 SRP060370 SRP060598 SRP061329 SRP061380 SRP061566 SRP061639
1 1 1 1 1 1 1 1 1 1 1 1 1 1
SRP061880 SRP062617 SRP063493 SRP063496 SRP063500 SRP064259 SRP064264 SRP064316 SRP064378 SRP064561 SRP064894 SRP066917 SRP066956 DRP001797
1 1 1 1 1 1 1 1 1 1 1 1 1 2
ERP003613 ERP003617 ERP004094 ERP006538 ERP008608 ERP009437 SRP000941 SRP007461 SRP012167 SRP018853 SRP020492 SRP034732 SRP041538 SRP041736
2 2 2 2 2 2 2 2 2 2 2 2 2 2
SRP042186 SRP043033 SRP044271 SRP049068 SRP050223 SRP056696 SRP057500 SRP058856 SRP059039 SRP060416 ERP005641 SRP001371 SRP006575 SRP011085
2 2 2 2 2 2 2 2 2 2 3 3 3 3
SRP040070 SRP048674 SRP049340 SRP051606 SRP055569 SRP066834 ERP001942 SRP026126 SRP027383 SRP048759 SRP048801 SRP053296 SRP053791 SRP056733
3 3 3 3 3 3 4 4 4 4 4 4 4 4
SRP067661 ERP005938 ERP008483 ERP010500 SRP010181 SRP056295 SRP057196 DRP002435 ERP001344 SRP049593 ERP011490 ERP012838 SRP025982 SRP063477
4 5 5 5 5 5 5 6 6 6 7 7 8 8
ERP012951 ERP009290 ERP003731 ERP012180
12 13 17 17
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Hi!
I'm using ReCount2 and it's very helpful and easy to use, I really appreciate all the effort. I was working with counts from SRP041538 and I realized that the file only contains 187 (of 189) samples, two samples are missing, SRR1265670 and SRR1265673. I was wondering if it's because of a quality issue or a mistake.
Thank you