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Forum: RNA Sequencing

05-29-2017, 12:19 AM

Replies: 9

Cannot use SRA data access in HISAT2

Views: 2,058

Posted By atonidas

I am following your advice and I put everything...

I am following your advice and I put everything back in there. Then I start compiling the "ngs-sdk.1.3.0-linux" again following the instruction and I got this message :

...

Forum: RNA Sequencing

05-26-2017, 05:52 AM

Replies: 9

Cannot use SRA data access in HISAT2

Views: 2,058

Posted By atonidas

I just checked the computer/bin directory, and...

I just checked the computer/bin directory, and there are uname and true command in here. it's here.

Forum: RNA Sequencing

05-26-2017, 01:53 AM

Replies: 1

cannot estimate transcript abundances in Stringtie

Views: 1,340

Posted By atonidas

cannot estimate transcript abundances in Stringtie

Here is the error :
stringtie –e –B -p 8 -G '/home/atonidas/RNAseq/chrX_data/samples/stringtie_merged.gtf' -o Alpha1.gtf '/home/atonidas/RNAseq/chrX_data/samples/Alpha1.bam'
Error: input file –e...

Forum: RNA Sequencing

05-26-2017, 01:29 AM

Replies: 9

Cannot use SRA data access in HISAT2

Views: 2,058

Posted By atonidas

I set /home/atonidas/bin as my $PATH and I did...

I set /home/atonidas/bin as my $PATH and I did installed all of my tools in there but there is no uname and true commands in that folder.

I have just installed ubuntu for 2 days and this is the...

Forum: RNA Sequencing

05-25-2017, 06:23 AM

Replies: 9

Cannot use SRA data access in HISAT2

Views: 2,058

Posted By atonidas

nope, I did not do that in MinW, I did that in...

nope, I did not do that in MinW, I did that in terminal of Linux. :confused:

Forum: RNA Sequencing

05-24-2017, 11:01 PM

Replies: 11

cannot copy samtools-0.1.19/samtools to PATH

Views: 1,995

Posted By atonidas

I have just installed linux and I could install...

I have just installed linux and I could install samtools without any problem anymore, thank you so much for your help. :D:D:D

Forum: RNA Sequencing

05-24-2017, 08:30 PM

Replies: 9

Cannot use SRA data access in HISAT2

Views: 2,058

Posted By atonidas

Cannot use SRA data access in HISAT2

everytime I try to run this command, i got this error :
$ hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran --sra-acc ERR188245 –S ERR188245_chrX.sam
hisat2-align-s: unrecognized option '--sra-acc'...

Forum: RNA Sequencing

05-23-2017, 07:47 AM

Replies: 11

cannot copy samtools-0.1.19/samtools to PATH

Views: 1,995

Posted By atonidas

I am using minGW/msys on win10

I am using minGW/msys on win10

Forum: RNA Sequencing

05-23-2017, 07:24 AM

Replies: 11

cannot copy samtools-0.1.19/samtools to PATH

Views: 1,995

Posted By atonidas

I think I got this error : bam_split.c:34:19:...

I think I got this error :
bam_split.c:34:19: fatal error: regex.h: No such file or directory
#include <regex.h>
^
compilation terminated.
make: *** [bam_split.o] Error 1
...

Forum: RNA Sequencing

05-23-2017, 07:19 AM

Replies: 11

cannot copy samtools-0.1.19/samtools to PATH

Views: 1,995

Posted By atonidas

Forum: RNA Sequencing

05-23-2017, 07:06 AM

Replies: 11

cannot copy samtools-0.1.19/samtools to PATH

Views: 1,995

Posted By atonidas

Do you mean that do I got any error when running...

Do you mean that do I got any error when running make command for samtools?

Forum: RNA Sequencing

05-23-2017, 05:39 AM

Replies: 11

cannot copy samtools-0.1.19/samtools to PATH

Views: 1,995

Posted By atonidas

I already tried with the latest version of...

I already tried with the latest version of "samtools" which is "samtools-1.4.1" but I still got that message :(:(:(

Forum: RNA Sequencing

05-23-2017, 05:23 AM

Replies: 11

cannot copy samtools-0.1.19/samtools to PATH

Views: 1,995

Posted By atonidas

cannot copy samtools-0.1.19/samtools to PATH

I am installing Samtools and I got this message:

$ tar jxvf samtools-0.1.19.tar.bz2
$ cd samtools-0.1.19
$ make
$ cd
$ cp samtools-0.1.19/samtools $HOME/bin
cp: cannot stat...

Forum: RNA Sequencing

05-23-2017, 04:53 AM

Replies: 2

cannot use "hisat2-build" command

Views: 2,009

Posted By atonidas

I have just installed Python and it's worked like...

I have just installed Python and it's worked like charm!

Thank you so much :D:D:D

Forum: RNA Sequencing

05-23-2017, 01:21 AM

Replies: 2

cannot use "hisat2-build" command

Views: 2,009

Posted By atonidas

cannot use "hisat2-build" command

Hello,

I use HISAT2 on msys environment of window and I’ve already downloaded the “hisat2-2.0.5-source.zip” and extract then :

$ export PATH=$HOME/bin:$PATH
$ cd hisat2-2.0.5
$ make
$ cd
$...

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