User: rizoic

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rizoic230
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Posts by rizoic

<prev • 21 results • page 2 of 3 • next >
4
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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 18 months ago by rizoic230
3
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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 18 months ago by rizoic230
0
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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 18 months ago by rizoic230
2
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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 18 months ago by rizoic230
1
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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 19 months ago by rizoic230
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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 19 months ago by rizoic230
0
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Answer: A: Error: Snakemake skiped a rule
... One of the problems I can see is that you have to add the output of rule `bowtie2Build` as input for rule `bowtie2Aln`. This way snakemake understands that it should perform the alignment only after the generation of the bowtie index. What it might do right now is execute the alignment step even b ...
written 19 months ago by rizoic230
4
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Answer: A: How to separate a strain of MTB drug wise?
... Incase you need a grep/awk based solution based on your tags. You can run something on these lines. If you paste the data into a file lets say `data.txt`. Example command for ` Pre-XDR` tail -n +2 data.txt |\ awk '{a[$1] = a[$1]","$2};END{for(i in a)print i"\t"a[i]}'|\ grep ISONIAZID| ...
written 19 months ago by rizoic230
3
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Answer: C: unable to load quant.sf files
... Can you add the output when you enter `files` on the terminal. You should not have both double/single quotes when you initialize files. Try removing the single quotes and changing the statement where you initialize files to `files <- c("/home/dell/Desktop/quant/quant3.sf", {same for other files}) ...
written 19 months ago by rizoic230
2
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Comment: C: R unused arguments, Biostrings
... You can use the code option in the formatting box to format your code for easier readability. One of the possibilities is that you have loaded another library which also has a translate function and that is the function being called. You can try being explicit with `Biostrings::translate()` and chec ...
written 19 months ago by rizoic230

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Teacher 18 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Supporter 19 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For C: unable to load quant.sf files
Teacher 19 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Scholar 19 months ago, created an answer that has been accepted. For C: unable to load quant.sf files
Teacher 19 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files

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