User: beginner

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beginner20
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Posts by beginner

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Comment: C: How to run simultaneous jobs in parallel using Job arrays in SLURM?
... yes there is R1 file also, in the above comment I showed only one. 110829_UNC11-SN627_0147_AD0DFWABXX.3_1.fastq ...
written 21 days ago by beginner20
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Comment: C: How to run simultaneous jobs in parallel using Job arrays in SLURM?
... When I did that I see this `-rw-rw-r-- seqware/lbginrc 12094029903 2014-01-09 23:15 110829_UNC11-SN627_0147_AD0DFWABXX.3_2.fastq` ...
written 21 days ago by beginner20
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Comment: C: How to run simultaneous jobs in parallel using Job arrays in SLURM?
... The actual tar.gz files looks different. They look like "UNCID_2207021.7b9569bc-f513-4b64-9a7c-7bb53b9be79b.110801_UNC12-SN629_0115_BD0DVEABXX_3_ACAGTG.tar.gz" But changed their names. ...
written 22 days ago by beginner20
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Comment: C: How to run simultaneous jobs in parallel using Job arrays in SLURM?
... I tried this before but it didn't work. And btw even untarring is taking more than 30 mins. ...
written 22 days ago by beginner20
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Comment: C: How to run simultaneous jobs in parallel using Job arrays in SLURM?
... yes, they were tarred. I want to untar them and use the fastq's for alignment all need to be done in a single script. Tar.gz files look like below: TCGA-A7-A0CH-11A.tar.gz TCGA-A7-A0DB-11A.tar.gz TCGA-A7-A0DC-11A_dd.tar.gz TCGA-A7-A0D9-11A.tar.gz ...
written 22 days ago by beginner20
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Comment: C: How to run simultaneous jobs in parallel using Job arrays in SLURM?
... I’m confused. Could you please explain with some script. ...
written 22 days ago by beginner20
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Comment: C: How to get rid of the temp files while using "featureCounts" for extracting rea
... No .tmp files are not deleted. I manually deleted them. ...
written 29 days ago by beginner20
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Comment: C: How to make the script work with stringtie command first and then merge the outp
... In the above way it gives an error. I submitted the job. ls: cannot access /path/*/*_GRCh38.gtf: No such file or directory Error: no transcripts were found in input file mergelist.txt ...
written 7 weeks ago by beginner20
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Comment: C: How to make the script work with stringtie command first and then merge the outp
... Yes, when ran the stringtie with bam files which I don't get in mergelist.txt works when I gave manually. ...
written 7 weeks ago by beginner20
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Comment: C: How to make the script work with stringtie command first and then merge the outp
... Is this what you want to me to change in the script? dir="/pathto/hisat2_output" dir2="/pathto/folder" for sample in /path/*.sorted.bam do base=`basename $sample '.sorted.bam'` "stringtie -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf \ -o ${dir2}/ ...
written 7 weeks ago by beginner20

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