User: rizoic

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rizoic190
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Posts by rizoic

<prev • 12 results • page 1 of 2 • next >
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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 5 weeks ago by rizoic190
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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 6 weeks ago by rizoic190
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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 6 weeks ago by rizoic190
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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 7 weeks ago by rizoic190
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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 7 weeks ago by rizoic190
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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 12 weeks ago by rizoic190
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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 3 months ago by rizoic190
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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 3 months ago by rizoic190
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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 3 months ago by rizoic190
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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 3 months ago by rizoic190

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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files
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Scholar 12 weeks ago, created an answer that has been accepted. For C: unable to load quant.sf files
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Scholar 3 months ago, created an answer that has been accepted. For C: unable to load quant.sf files
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: unable to load quant.sf files

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