Moderator: genomax

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genomax64k
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Posts by genomax

<prev • 11,392 results • page 2 of 1140 • next >
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Comment: C: Java error message when using BBDuk
... `bbduk.sh` should not need 80g of RAM. Can you try running this with a smaller number of threads (`t=4` and `-Xmx5g`). Are you input files already trimmed for adapters and you are now doing quality trim? ...
written 23 hours ago by genomax64k
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Comment: C: How to get the pathway-protein relationship?
... What have you tried so far? It would be good to know so people don't recommend things you have already tried. ...
written 23 hours ago by genomax64k
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Comment: C: UpSet plots in R
... Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. Thank you! ...
written 23 hours ago by genomax64k
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Answer: A: Query bacterial genus on NCBI from a list of accessions
... Using [Entrezdirect][1] $ more acc NZ_JRTV01000009.1 NZ_CEWL01000009.1 NZ_CP013481.2 NZ_CP009553.3 NZ_CBYD010000018.1 NZ_CBYE010000015.1 NZ_CP016370.1 $ epost -db nuccore -input acc | esummary | xtract -pattern DocumentSummary -element Caption,Organism N ...
written 1 day ago by genomax64k
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Comment: C: MiRdeep2 for paired-end RNA-seq?
... miRNA data generally needs some specific processing (removal adapters etc). Please see instructions for the kit you used and pre-process your data before trying to align it. ...
written 1 day ago by genomax64k
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Comment: C: Convert Gene IDs of Tomato Sol Database
... You can post the file up on pastebin.com or as a gist on github.com. Then post the link in your answer from yesterday. ...
written 1 day ago by genomax64k
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Comment: C: Java error message when using BBDuk
... Can you validate your fastq files using validateFiles utility [here][1]? Remeber to do `chmod a+x validateFiles` after you download. [1]: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/validateFiles ...
written 1 day ago by genomax64k
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Comment: C: Low Mapping percentage with Minimap2 due to contamination
... Since you have long reads you are probably going to be limited in tools you can use for screening for contamination that are currently available. `kraken` (https://ccb.jhu.edu/software/kraken2/ ) is generally used for this, but I am not sure if it will accept long reads. You could use `shred.sh` fr ...
written 1 day ago by genomax64k
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Answer: A: Removing last characters of sequence names in a FASTA
... Try this: cut -d "." -f1 your_file > new_file ...
written 1 day ago by genomax64k
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Comment: C: Downsample BAM for targeted NGS panels
... You can easily test it with sampling a small number of reads. You can also try`reformat.sh` from BBMap to do subsampling. I think it should work with a BAM file. You will have a rich set of options for sampling ...
written 1 day ago by genomax64k

Latest awards to genomax

Scholar 20 hours ago, created an answer that has been accepted. For A: Query bacterial genus on NCBI from a list of accessions
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Removing last characters of sequence names in a FASTA
Scholar 1 day ago, created an answer that has been accepted. For A: Removing last characters of sequence names in a FASTA
Scholar 1 day ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Scholar 1 day ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Scholar 4 days ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Teacher 6 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Teacher 8 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Teacher 8 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Scholar 8 days ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Scholar 10 days ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Teacher 14 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Commentator 14 days ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?
Teacher 17 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Scholar 17 days ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Scholar 20 days ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Teacher 20 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Google genomics cloud platform ?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Scholar 5 weeks ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?

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