User: dimitrischat

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dimitrischat30
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Posts by dimitrischat

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Comment: C: input of cummerbund
... is there an option for that in the command line ? because i (prefer) ran cuffdiff in terminal. many thanks edit: or manipulate yourself the output(s) of cuffdiff to make an sqlite file? ...
written 11 days ago by dimitrischat30
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Comment: C: input of cummerbund
... ok thank you. i will read it through ...
written 11 days ago by dimitrischat30
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input of cummerbund
... Hello all. I finally ran cuffdiff successfully, but now i wanna run cummeRbund on galaxy. i have no idea which of the outputs i must use. do i have to do something now or i had to put an option when cuffdiff ran so i had a specific output for cummeRbund? ...
rna-seq written 11 days ago by dimitrischat30 • updated 11 days ago by e.rempel200
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Comment: C: cuffmerge no such file or directory
... it was correct. i retyped the name-file and it worked. no idea what was wrong. something with unicode, some character of the file name was ..like an error...dont know ...
written 11 days ago by dimitrischat30
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cuffmerge no such file or directory
... trying to run cuffmerge in mac os. when i had 2 samples it worked. when i had 16 it doesnt. it comes up with this error : Traceback (most recent call last): File "/usr/local/bin/cuffmerge", line 580, in sys.exit(main()) File "/usr/local/bin/cuffmerge", line 538, in main ...
rna-seq written 16 days ago by dimitrischat30 • updated 16 days ago by WouterDeCoster20k
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cuffdiff / htseq-count
... Hello all. I ll try and be clear this time around about what i am asking. I am trying to run cuffdiff. Before i ran tophat2, got the accepted hits then sorted them and then put them into cuffdiff. my command line is this : cuffdiff -o /Users/.../cuffdiffmefrep1-rep2/ -L mef1,mef2 -p 2 ~/.../mm9gen ...
rna-seq written 7 weeks ago by dimitrischat30 • updated 7 weeks ago by Devon Ryan69k
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problem running cufdiff
... Hello all. Trying to run cuffdiff : cuffdiff -p 2 -L esred1,esred2 -o /Users/../cuffdiff /Users/Desktop/RNA\ seq/gtf/Mus_musculus.GRCm38.88.chr.gtf /Users//accepted-red1.sam /Users/accepted-red2.sam and returning error : cuffdiff(4756,0x7fffee9c33c0) malloc: *** mach_vm_map(size=35472337879373127 ...
rna-seq written 11 weeks ago by dimitrischat30
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Comment: C: cufflinks/cuffdiff command line
... whitespace is ...\ .. right ? also if i cant run cufflinks how will i get the trascripts .gtf file? "produced by cufflinks" .. sorry i guess its a "stupid" question . Thanks for your reply ...
written 12 weeks ago by dimitrischat30
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cufflinks/cuffdiff command line
... i ve been trying to figure out the command line for cufflinks/cuffdiff but i have been getting error again and again. Trying the command line with 2 bam files from tophat : cuffdiff -p 2 --labels esred1,esred2 - b /Users/../mm9genome.fa /Users/.../accepted_hits-red1.bam,/Users/.../accepted_hi ...
rna-seq written 12 weeks ago by dimitrischat30 • updated 12 weeks ago by Ram12k
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Comment: C: Reduce/Select reads/lines ffrom files using terminal
... the first link is about splitting, i want to select the first x lines from the fastq file ...
written 3 months ago by dimitrischat30

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