User: garentguuu

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garentguuu10
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Posts by garentguuu

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Comment: C: Cufflinks dependency problem error - Solution: use version 2.2.1.2 or later
... Dear Jennifer, Thanks for you reply. As your advise, I have checked all parameters with Galaxy, it is still not the same. My line-command result still has very low value, also my cufflinks version is v2.2.1. I am curious about the 3rd party: "tool's computational core is not modified", how can I mo ...
written 26 days ago by garentguuu10
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Comment: C: Cufflinks dependency problem error - Solution: use version 2.2.1.2 or later
... Dear Jennifer, Thanks for your help. It works now, however, I have another question about the cufflinks. When I tried the cufflinks in Galaxy, the result showed the lowest gene expression is no more than 0.00005, but I had tried on cufflinks tool downloaded from their official sites, I found the re ...
written 28 days ago by garentguuu10
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Cufflinks dependency problem error - Solution: use version 2.2.1.2 or later
... Hi, Recently, I met an error when I tried the cufflinks in Galaxy. It reports an error: Traceback (most recent call last): File "/jetstream/scratch0/main/jobs/20147175/tool_files/cufflinks_wrapper.py", line 9, in from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attr ...
galaxy cufflinks rna-seq written 29 days ago by garentguuu10 • updated 28 days ago by Jennifer Hillman Jackson25k
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cufflinks in Galaxy
... Hi, Recently, I tried to use cufflinks in Galaxy. However, it is running several days and never finished. Because I had used cufflinks before in Galaxy, it run no more than one days. Then I checked my bam file, it is only 2 G. Anyone knows what's the problem of cufflinks in Galaxy? Thank you! ...
galaxy cufflinks rna-seq written 10 weeks ago by garentguuu10 • updated 10 weeks ago by Jennifer Hillman Jackson25k
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Hisat2 to cufflinks
... Hi, Recently, I tried use hisat2 to mapping RNA-seq, then use cufflinks to measure the gene expression in galaxy. I am curious about the step after hisat2. If I finished hisat2, should I need use to samtools to sort the bam file? Because I did not sort the output of hisat2, and it run well in cuffl ...
galaxy cufflinks rna-seq written 3 months ago by garentguuu10 • updated 3 months ago by Jennifer Hillman Jackson25k
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Answer: A: galaxy_filter_sam report error
... Thanks for you help. After I sorted the bam, it works well. Thank you! Garen ...
written 3 months ago by garentguuu10
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galaxy_filter_sam report error
... Hi, Recently, I try to use samtools: Filter SAM or BAM, output SAM or BAM, but it reported that: ############################# Set it manually or retry auto-detection [E::hts_idx_push] Chromosome blocks not continuous ############################## I don't know what is wrong with ...
bam samtools galaxy sort picard written 3 months ago by garentguuu10
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Question: Trim Galore in Galaxy cannot work
... Hi, everyone, I have a problem about Galaxy trim galore tools. When I download data from SRA, Galaxy report the error: 1.8 Cutadapt terminated with exit signal: '256'. Terminating Trim Galore run, please check I don't know what happened with this tools. The input file is fastqsanger.gz from SRA. ...

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