User: rizoic

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rizoic200
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Posts by rizoic

<prev • 15 results • page 1 of 2 • next >
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Answer: C: .bash_profile shortcut to reverse a string
... You just need to remove the alias in your function and change the first argument to $1 as you are not interested in the length i.e. $#1 ``` revFunc() { echo ${1}|rev } ``` For reverse compliment you can change the function to be ``` revComp() { echo ${1}|tr "[ATGCatgc]" "[TACGtacg]"|r ...
written 4 weeks ago by rizoic200 • updated 4 weeks ago by RamRS23k
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Comment: C: Expression values for normal tissues
... Thanks. Z scores should give me a good idea about high/low expressed genes in the tumor. By chance are you aware of any resource to get an idea about the status of these genes in normal tissues? ...
written 8 weeks ago by rizoic200
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Expression values for normal tissues
... We have RNA seq `transcripts per million(TPM)` values for all genes in a tumor patient sample. However there was no sequencing done for normal samples from the same patient. We want to determine which genes are being over/under expressed in the tumor and having just its expression values is obviousl ...
rnaseq written 8 weeks ago by rizoic200 • updated 8 weeks ago by Kevin Blighe46k
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Comment: C: How to remove singletons in a BAM file using samtools
... In your e.g. R1 is the singleton read since its mate is unmapped and thus R1 read will be removed when you filter for the flag `0x08`. ...
written 8 months ago by rizoic200
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Answer: C: How to remove singletons in a BAM file using samtools
... As per the [SAM flag guide][1] the flag that you are filtering for i.e. `0x04` is for unmapped reads. This explains the removal of unmapped reads. In case you want to filter for singletons i.e. reads for which the `mate is unmapped` you an select that as the condition. This gives a SAM flag value ...
written 8 months ago by rizoic200
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Answer: C: Filter DNA sequence in FASTA file by minimum length and redirect sequences that
... In case it is a requirement to do the solution without any additional packages then you can use the solution by Heather. However when parsing standard file formats it is always recommended to use specialized packages for handling them. You can use the `Biopython` package in python for this. An examp ...
written 8 months ago by rizoic200
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Comment: C: How to separate a strain of MTB drug wise?
... For Pre-XDR as per the condition you mention i.e. `Isoniazid, Rifampicin and (CIPROFLOXACIN|MOXIFLOXACIN|OFLOXACIN|LEVOFLOXACIN) any of these or one or two depends.` the command should be the same as in the answer right? i.e. tail -n +2 data.txt |\ awk '{a[$1] = a[$1]","$2};END{for(i in a)p ...
written 8 months ago by rizoic200
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Comment: C: What is the best way to compare transcriptome between different condition?
... If you are interested in just knowing which of the knockdowns i.e. B or C is close to lets say A, you can do hierarchical clustering on the counts post applying a transform like `vst() or rld()` in DEseq2. You can find an example [here][1]. [1]: http://people.duke.edu/~ccc14/duke-hts-2017/Statis ...
written 9 months ago by rizoic200
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Comment: C: How to separate a strain of MTB drug wise?
... A simplistic tweak would be to change the condition on these lines tail -n +2 data.txt |\ awk '{a[$1] = a[$1]","$2};END{for(i in a)print i"\t"a[i]}'|\ grep -P "\t,ISONIAZID,RIFAMPICIN$" Here the -P makes grep evaluate the expression as a perl compatible regex.The `\t and $`(indicating ...
written 10 months ago by rizoic200
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Comment: C: Error: Snakemake skiped a rule
... Changing rule bowtie2Aln: input: rules.trimmen.output To rule bowtie2Aln: input: rules.trimmen.output, rules.bowtie2Build.output Should solve this error for you. It would be better to state an explicit dependency than specifying a priority in this case. You can use the `--dry ...
written 10 months ago by rizoic200

Latest awards to rizoic

Teacher 8 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Supporter 10 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For C: unable to load quant.sf files
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Scholar 10 months ago, created an answer that has been accepted. For C: unable to load quant.sf files
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files

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