User: RBright21

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RBright2110
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Posts by RBright21

<prev • 17 results • page 1 of 2 • next >
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Comment: C: bedtools genomecov max function not working correctly
... Thank you - I hadn't noticed that bit. It does work though - completely on some of my bam files with the same parameters set and across the majority of the rest of the files with the exception of the last base or two though? Surely if it didn't work for those options then my files would be reportin ...
written 4 days ago by RBright2110
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bedtools genomecov max function not working correctly
... When using bedtools genomecov max function I get values reported for some chromosomes/reference sequences which are above the max depth set. This is not consistent between files and always occurs on the last base or two of the reference genome. The number of chromosomes affected varies between bam f ...
bedtools assembly genomecov written 4 days ago by RBright2110 • updated 4 days ago by ATpoint45k
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Comment: C: Bowtie 2 warning when outputting unmapped reads
... Perfect - thanks very much. In hindsight I should have checked some links further down on google as I clearly see this now. Could have saved myself some time! ...
written 6 days ago by RBright2110
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Bowtie 2 warning when outputting unmapped reads
... I have been using bowtie2 to align 150bp illumina miseq reads to a reference genome and would like to output unmapped reads to a separate file for further investigation. I have tried using the command below (all and local are selected for my application) bowtie2 -a --local -x index -1 R1.fastq. ...
bowtie2 alignment written 6 days ago by RBright2110 • updated 6 days ago by ATpoint45k
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Comment: C: Should you include Trimmomatic unpaired reads when assembling by alignment?
... I am trying to identify virus strain so your suggestion is really helpful. I do have lots of data and its only a 36kb genome so I do find when I align my reads I have lots of coverage and haven't found an instance yet where leaving out the unpaired reads has been detrimental. When I first started ex ...
written 8 days ago by RBright2110
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Comment: C: Should you include Trimmomatic unpaired reads when assembling by alignment?
... Thanks so much for your quick response again. It is viral DNA (enriched during the library prep to remove non-target sequences) and illumina paired end reads (generated on Miseq) that I am working with. Should I be considering using the "keepbothreads" function in Trimmomatic if I see discard rate ...
written 8 days ago by RBright2110
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Comment: C: Should you include Trimmomatic unpaired reads when assembling by alignment?
... Hi Michael Apologies I'm still very new to bioinformatics so I'm not always sure on the terminology - I was thinking when using an alignment tool like Bowtie2 for alignment of reads against a reference sequence. Thanks for your input though. What would you consider to be a large fraction of unpair ...
written 8 days ago by RBright2110
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Should you include Trimmomatic unpaired reads when assembling by alignment?
... Should you include unpaired reads generated from adaptor/quality trimming using Trimmomatic when carrying out assembly by alignment? I had thought that you should so as not to lose what could be valuable data but have been reading recently that some people discard unpaired reads prior to analysis. ...
assembly sequence alignment written 8 days ago by RBright2110
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Comment: C: Sequence Duplication Levels and Clumpify
... HI Genomax, I just ran some files quickly through BB norm and it did improve the number of contigs generated. I'll continue to have a play with it and see how I get on. Thanks for your help ...
written 23 days ago by RBright2110
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Comment: C: bcftools consensus equivalent for VarScan output
... Hi Kevin Thanks so much for this, its really helpful. I will have a go back through the manual with this information and see what I can achieve. ...
written 23 days ago by RBright2110

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