Moderator: genomax2

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genomax222k
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Posts by genomax2

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Comment: C: help - .fam and .bim kept being automatically converted to .txt by Mac
... Remove the `.txt` extension by renaming the files. That should be all that is needed, if you are downloading them from web? ...
written 1 day ago by genomax222k
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Comment: C: I want to know about the actual function of Bowtie?
... Take a look at figure 1 in the [Nature methods protocol][1] that describes the TopHat suite in detail. Index creation is an essential step in the preparation of reference genomes for NGS alignment. It needs to be done only once (`bowtie2-build` process). Once the index files are ready they are re-u ...
written 1 day ago by genomax222k
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Comment: C: gene comparison between different species
... NCBI may have already done the work for you. Take a look at [homologene][1]. [1]: https://www.ncbi.nlm.nih.gov/homologene ...
written 1 day ago by genomax222k
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Comment: C: SOLVED: Having trouble installing Bioconductor package GEOquery
... You can go ahead and accept this answer (green check mark) to provide closure to this thread. ...
written 1 day ago by genomax222k
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Comment: C: 10x Supernova de novo assembly
... Was this a human sample? One I had ended up at ~1.6 Gb. ...
written 1 day ago by genomax222k
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Comment: C: remove out short predict genes from gff file
... If you want to only remove `mRNA` line then: `awk '{if (($5 - $4)> 150 || ($3 == "exon")) print $0}' your_file > new_file`. If you want to only keep `mRNA` line then: `awk '{if (($5 - $4)> 150 || ($3 == "mRNA")) print $0}' your_file > new_file` ...
written 1 day ago by genomax222k
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Comment: C: remove out short predict genes from gff file
... How about: `awk '{if (($5 - $4)> 150) print $0}' your_file > new_file` Adjust `150` to a value that will exclude things smaller than that length. ...
written 1 day ago by genomax222k
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Answer: C: Having trouble installing Bioconductor package GEOquery
... See if [this helps][1]? You may still be better off using another lightweight linux distro instead of one meant for use on Pi on this laptop. [1]: https://www.raspberrypi.org/forums/viewtopic.php?t=111375&p=767299 ...
written 1 day ago by genomax222k
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Comment: C: Having trouble installing Bioconductor package GEOquery
... Are you trying to do this on a raspberry Pi? I doubt there is enough RAM on the Pi to do useful bioinformatics (or install packages). ...
written 2 days ago by genomax222k
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Comment: C: I want to know about the actual function of Bowtie?
... Yikes! You are using a very old version of TopHat (2+ years). So the first thing to try would be to upgrade that. Your bowtie2 is also not the latest so upgrade it while you are at it. TopHat will take care of the actual bowtie2 alignments as long as you have bowtie2 available and properly install ...
written 2 days ago by genomax222k

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Scholar 1 day ago, created an answer that has been accepted. For A: can anyone explain pipes in blastn output
Scholar 2 days ago, created an answer that has been accepted. For A: can anyone explain pipes in blastn output
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?
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Scholar 4 days ago, created an answer that has been accepted. For C: Suggestions on Sharing VERY LARGE files?
Popular Question 9 days ago, created a question with more than 1,000 views. For NovaSeq from Illumina (updated info)
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?
Scholar 11 days ago, created an answer that has been accepted. For C: Suggestions on Sharing VERY LARGE files?
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: Google genomics cloud platform ?
Scholar 19 days ago, created an answer that has been accepted. For A: can anyone explain pipes in blastn output
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?
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Teacher 27 days ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Google genomics cloud platform ?
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Scholar 5 weeks ago, created an answer that has been accepted. For A: can anyone explain pipes in blastn output
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Better for my career: Degree in computer science or Phd in bioinformatics?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do you cite a tool that doesn't have a publication?
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Scholar 6 weeks ago, created an answer that has been accepted. For A: can anyone explain pipes in blastn output
Scholar 6 weeks ago, created an answer that has been accepted. For A: can anyone explain pipes in blastn output

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