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  • Mar 24 2016 17:46
    bmlewis-UCSD synchronize #107
  • Mar 15 2016 23:44
    apryan opened #130
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  • Mar 07 2016 00:05
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Olga Botvinnik
@olgabot
I didn’t want you making a new branch or somethign
vwfu
@vwfu
nope haha
thanks !
LElmen
@LElmen
For the FPKM calculation, where do we get the total number of reads sequenced? The defined reads = from the bam is the read counts of feature of interest, isn't it?
ecwheele
@ecwheele
Sum the values in the column of feature counts
Those are the total number of reads that mapped to genes. Each Fragment mapped to a gene comes from 1 read
So there are also sequencing reads that don't map to genes, but in this case we are not interested in them so we take the total sum of fragments (reads) that mapped to genes by summing that column in the featurecounts output
LElmen
@LElmen
what is the header of the feature counts output, I might be missing columns
mbaughn
@mbaughn
I was too
ecwheele
@ecwheele
it should be the last column that is labelled /home/ucsd-trainxx/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam
LElmen
@LElmen
No, I have it! Thank you both!
LElmen
@LElmen
I don't get it... If FPMK= "counts observed for feature x" (which is the sum of the /...//sorted.bam)/ length (summed up length column) * Total reads sequenced,
where are the total reads sequenced no?
ecwheele
@ecwheele
FPKM = ((counts to a gene / length of the gene) / total reads sequenced)* 1e9
total reads sequenced is the sum of the counts column
which you can get with:
reads = s10_featurecounts['/home/ucsd-trainxx/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam']
total counts = reads.sum()
LElmen
@LElmen
Finally got it... I've been trying to sum up ALL genes and counts here... (For once syntax wasn't the problem). I should probably not try to do any calculations ever after 10pm. If I take the example gene given in the assert it matches now. Thank you!!\
mbaughn
@mbaughn
If anyone is suspicious of their symbolic links, you can print their paths using the -H option of ls:
E.G.
[ucsd-train03@tscc-login1 scratch]$ ls -lhaH

lrwxrwxrwx   1 ucsd-train03 biom262-group   27 Feb  8 09:17 shalek2013 -> /home/ucsd-train03/projects
mbaughn
@mbaughn
also
tree -f
is like " ls methadone" for the GUI-addicted
I will never again just keep mashing cd… ls… cd… ls… to dive down into nested folders and figure out where things are
tree -f then copy paste the full path and cd there
ecpierce
@ecpierce
Has Oliviers homework been assigned/when is it due?
ericsan119
@ericsan119
Does anyone know how to install Varscan on TSCC?
mbaughn
@mbaughn
Module load biotools?
mbaughn
@mbaughn
Nope, nm… definitely not that
[tscc-login1 ps-yeolab]$ tree -f | grep 'varscan'
│   │   │   ├── ./biom262-2015/biom262_harismendy/class1/varscan.err
│   │   │   ├── ./biom262-2015/biom262_harismendy/class1/varscan.out
│   │   │   └── ./biom262-2015/biom262_harismendy/class1/varscan.sh
│   │   │   └── ./biom262-2015/biom262_harismendy/resources/varscan_dna_copy_rcode.r
│   │   ├── ./biom262-2015/biom262_harismendy/varscan
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CNA.out.copynumber
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/countcommand.txt
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES14.pileup
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1.pileup
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_DNACopy_merged.copynumber
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc_failed.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc_germlineLOH.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc_somatic.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered.indel
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14.indel
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_totalPassed_somatic_coding.table
│   │   │   └── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_totalPassed_somatic.table
│   │   ├── ./biom262-2015/tools/varscan
│   │   │   ├── ./biom262-2015/tools/varscan/fpfilter.pl
│   │   │   ├── ./biom262-2015/tools/varscan/mergeSegments.pl
│   │   │   └── ./biom262-2015/tools/varscan/VarScan.v2.3.7.jar
│   │   │   └── ./biom262_2016/data/PBSscripts/varscan.sh
│       ├── ./biom262_2016/tools/varscan
│       │   └── ./biom262_2016/tools/varscan/VarScan.v2.3.9.jar
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found it!
java -jar /projects/ps-yeolab/biom262_2016/tools/varscan/VarScan.v2.3.9.jar
at least that is the directory we used in class
ericsan119
@ericsan119
Thanks~
Yiren Hu
@Charlottehu
@olgabot just to clarify, for the exam question 1.3) a) , are we going to merge these two files and give a single answer or give separate answers for each file?
Jamison M McCorrison
@bioh4x
Hi Charlotte, For 1.3, it is intended that you provide answers for each file separately, though I would accept the merged file solution as long as the unix methods are provided!
andersonbrookee
@andersonbrookee
Any words of advice on this?
Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
Happens when I try to use anything with java, including java -jar, java -version, and java -help
andersonbrookee
@andersonbrookee
nvm turns out I don't need that to run.
andersonbrookee
@andersonbrookee
still getting issues trying to run vcffilter though. Keep getting a ton of
Input stream not ready, waiting for 5 seconds...
before it just aborts
Jamison M McCorrison
@bioh4x
It looks like it might be caused by the order your flags are included? ( https://sourceforge.net/p/varscan/discussion/1073559/thread/27563361/ )
Olga Botvinnik
@olgabot
Hey for running java jobs you need to be in an interactive node because they require so much memory
Ie submit an interactive job and then run the command
Or submit a script with the command
Shicheng Guo
@Shicheng-Guo
great