User: emcc

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emcc10
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2 weeks, 2 days ago
Joined:
7 months ago
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e**********@qub.ac.uk

Posts by emcc

<prev • 8 results • page 1 of 1 • next >
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Comment: C: HISAT output SAM file incorrect (only contains 3 columns of data)
... Apologies, I clearly didn't scroll for long enough. I have the expected content further down the file. Thank you so much for your time- I'm new to this and I really appreciate the help. ...
written 6 months ago by emcc10
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HISAT output SAM file incorrect (only contains 3 columns of data)
... Hello, I have ran into to various problems in the HISAT-StringTie pipeline and have traced it back to incomplete SAM file output from the initial mapping. I generated the indicies myself (job out complete and gave 8 .ht2 files of binary content). My read files are called in .gz archive file format ...
files hisat sam written 6 months ago by emcc10
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Comment: C: Stringtie GTF naming convention error
... Changed. Thank you :) ...
written 6 months ago by emcc10
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Comment: C: Stringtie GTF naming convention error
... I used the commands cat genome.fa ERCC.fa >genome_ERCC.fa cat genome.gtf ERCC.gtf >genome_ERCC.gtf these outputs were used to build the index used for alignments. I have since run the pipeline with the basic genome files (not including ERCC seqs) and I get the same problem. Could th ...
written 6 months ago by emcc10
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Stringtie GTF naming convention error
... I have looked through similar posts with the same warning: > WARNING: no reference transcripts were found for the genomic sequences > where reads were mapped! Please make sure the -G annotation file uses > the same naming convention for the genome sequences. The indexes were built using t ...
gtf stringtie naming convention written 6 months ago by emcc10
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Comment: C: HISAT index incomplete even with HUGE RAM
... Thank you I needed to request access to a 1TB node and the settings below then worked. Thanks again for your help :-) > > #$ -pe smp-verbose 8 > > #$ -l h_vmem=125G > > #$ -l himem=true ...
written 6 months ago by emcc10
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Comment: C: HISAT index incomplete even with HUGE RAM
... Thank you Devon, I didn't realise about the nodes, I was kind of "throwing the kitchen sink at it" by requesting as much processing memory as possible as various other attempts have not worked. I have used your exact instructions, and: #$ -pe smp-verbose 8 #$ -l h_vmem=64G And fur ...
written 7 months ago by emcc10
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HISAT index incomplete even with HUGE RAM
... Hello, I'm hoping someone can help. I'm attempting to create index files for a species not available on the pre-made list and continually getting errors associated with memory. I have allocated 480GB RAM (for a 1.3GB genome) on a HPC cluster and it produces 6 of the 8 ht2 files (file 5 and 6 missi ...
hisat index indexing written 7 months ago by emcc10 • updated 7 months ago by Devon Ryan84k

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