Dear colleague,
I was looking at the MSBB Data Descriptor paper (https://www.nature.com/articles/sdata2018185). Seems that there are less samples in syn8612191 than what the authors listed in supplementary table 1 (https://media.nature.com/original/nature-assets/sdata/2018/sdata2018185/extref/sdata2018185-s2.xlsx). Specifically these samples are not in syn8612191:
```
[1] "hB_RNA_13477" "BM_10_788" "hB_RNA_13294" "hB_RNA_4811" "hB_RNA_4841"
[6] "BM_22_11" "hB_RNA_4851" "hB_RNA_13397" "hB_RNA_4862" "BM_10_553"
[11] "hB_RNA_16925" "BM_22_178" "hB_RNA_4871" "hB_RNA_10432" "BM_36_389"
[16] "BM_10_765" "hB_RNA_9136" "hB_RNA_4881" "hB_RNA_12651" "hB_RNA_8515"
[21] "BM_10_796" "hB_RNA_4891" "BM_10_554" "BM_22_254" "BM_36_415"
[26] "hB_RNA_16735" "BM_10_555" "hB_RNA_13418" "BM_22_126" "hB_RNA_9139"
[31] "hB_RNA_4919" "hB_RNA_7995" "hB_RNA_7995" "hB_RNA_13373" "hB_RNA_13373"
[36] "BM_22_101" "hB_RNA_9140" "hB_RNA_4932" "BM_10_700" "hB_RNA_12680"
[41] "hB_RNA_11012" "hB_RNA_11012" "hB_RNA_12774" "hB_RNA_7925" "hB_RNA_10512"
[46] "hB_RNA_8525" "hB_RNA_12934" "hB_RNA_8015" "hB_RNA_10702" "hB_RNA_8385"
[51] "hB_RNA_12768" "hB_RNA_9144" "hB_RNA_7755" "hB_RNA_9196" "BM_10_695"
[56] "BM_22_162" "BM_36_284" "hB_RNA_16525" "BM_10_673" "BM_36_324"
[61] "hB_RNA_13491" "hB_RNA_9199" "BM_36_325" "hB_RNA_12302" "hB_RNA_12302"
[66] "hB_RNA_5001" "hB_RNA_5001" "BM_10_802" "BM_36_407" "hB_RNA_5011"
[71] "hB_RNA_9201" "hB_RNA_5021" "BM_10_789" "hB_RNA_9202" "hB_RNA_8355"
[76] "hB_RNA_12744" "hB_RNA_12744" "hB_RNA_10992" "BM_36_330" "BM_22_186"
[81] "BM_36_355" "BM_36_360" "hB_RNA_12588" "BM_22_245" "hB_RNA_9226"
[86] "hB_RNA_8675" "hB_RNA_9229" "BM_10_684" "BM_22_171" "BM_36_380"
[91] "hB_RNA_16465" "hB_RNA_9184" "hB_RNA_8485" "BM_36_331" "hB_RNA_12392"
[96] "hB_RNA_12392" "BM_22_187" "hB_RNA_16905" "hB_RNA_16895" "BM_10_687"
[101] "hB_RNA_8935" "hB_RNA_12695" "hB_RNA_11002" "hB_RNA_7835" "hB_RNA_7835"
[106] "hB_RNA_8855" "hB_RNA_12624" "hB_RNA_8805" "hB_RNA_8965" "hB_RNA_13340"
[111] "BM_36_346" "hB_RNA_9146" "hB_RNA_13616" "BM_22_147" "hB_RNA_9147"
[116] "hB_RNA_4371" "BM_36_332" "hB_RNA_8435" "hB_RNA_9149" "hB_RNA_4398"
[121] "BM_10_727" "BM_36_364" "BM_36_381" "BM_36_333" "BM_36_340"
[126] "BM_10_558" "BM_22_146" "BM_36_337" "hB_RNA_16455" "BM_10_603"
[131] "hB_RNA_4437" "BM_10_557" "hB_RNA_9153" "BM_36_444" "hB_RNA_9165"
[136] "BM_10_760" "hB_RNA_9167" "BM_22_42" "hB_RNA_9183" "hB_RNA_10342"
[141] "hB_RNA_10382" "hB_RNA_8815" "BM_36_289" "hB_RNA_8695" "hB_RNA_9005"
[146] "BM_10_805" "BM_10_662" "hB_RNA_9181" "hB_RNA_8615" "hB_RNA_13309"
[151] "BM_22_83" "BM_36_496" "hB_RNA_4551" "BM_10_799" "BM_22_84"
[156] "hB_RNA_16965" "BM_10_781" "BM_36_420" "BM_22_93" "BM_22_251"
[161] "BM_36_336" "hB_RNA_4623" "BM_22_105" "hB_RNA_4631" "BM_36_342"
[166] "BM_22_31" "hB_RNA_9182" "BM_10_598" "hB_RNA_13430" "hB_RNA_8025"
[171] "BM_10_636" "hB_RNA_13441" "BM_36_387" "hB_RNA_13330" "BM_36_296"
[176] "hB_RNA_12332" "BM_10_606" "BM_10_667" "hB_RNA_13320" "BM_36_329"
[181] "BM_10_708" "hB_RNA_4720" "BM_22_164" "hB_RNA_4728" "BM_10_742"
[186] "hB_RNA_9187" "hB_RNA_9187" "BM_10_674" "hB_RNA_9189" "BM_10_627"
[191] "hB_RNA_9190" "hB_RNA_9190" "BM_10_620" "BM_22_145" "hB_RNA_9193"
[196] "hB_RNA_13609" "hB_RNA_4782" "hB_RNA_4782"
```
Do you have a plan to update syn8612191 (or the parent folder) so they can match with the paper?
Thank you very much for your help.
Guoqiang Zhang
Created by Guoqiang Zhang guoqiangzhang Reposting this on the thread
The fastq files are the ones from an initial sample QC of this data. A later more thoughrough QC rescued some of the files. The fastq were created from bam files (where the unmapped reads have also been provided). We are reviewing to make sure we have all the bams referenced in the paper. The missing fastq can then be created from the existing bams
Drop files to upload
additional RNAseq data for the MSBB cohort syn8612191 page is loading…