User: toralmanvar

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toralmanvar900
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Posts by toralmanvar

<prev • 193 results • page 1 of 20 • next >
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Comment: C: heatmap GSEA software
... It will not be fair to say DESeq2 is more reliable. It totally depends upon the type of samples and number of replicates you are working with. [This][1] paper can give you more insight. [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8 ...
written 7 weeks ago by toralmanvar900
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Comment: C: Filtering already published SNP data
... That depends on your need. If you find filtering parameters provided in publication satisfactory then there is no further need to filter it but if you wish to change it then you can use [vcftools][1] for any modification. For eg: If SNPs were filtered using MAF<0.05 and you want it as MAF<0.1 ...
written 7 weeks ago by toralmanvar900
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Comment: C: "MethylKit" package for WGBS data
... It seems methylkit was not able to find anything common between 5 samples. Is your input file tab delimited? If yes try providing seperator as **sep = "\t"** . ...
written 7 weeks ago by toralmanvar900
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Comment: C: RNASeq, gtf file
... Ok got it. Thank you very much for this. ...
written 7 weeks ago by toralmanvar900
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Comment: C: RNASeq, gtf file
... Hello juke34, I have not used the suggestion given by you, but was curious to know that whether this script will be able to remove all exons associated with transcripts. I am asking this as there is no FPKM information available for exon. ...
written 7 weeks ago by toralmanvar900
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Comment: C: *.misa and *.statistic file differ in the identified ssr.
... That depends on your aim. However, you can always report whatever is obtained in .statistics file. ...
written 7 weeks ago by toralmanvar900
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Answer: A: *.misa and *.statistic file differ in the identified ssr.
... What you are getting in .statistics and .misa is correct. Number of SSRs in detail file are equal to following: Total number of identified SSRs - Number of SSRs present in compound formation See here for example: Total number of sequences examined 740501 Total size of examined sequence ...
written 8 weeks ago by toralmanvar900
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Comment: C: What organism's genome should be used in FastQ Screen
... During mapping process any reads originating from any other source will not map to *Physomitrella patens* genome and thus contamination will be removed automatically. If you get very less % mapping on *Physomitrella patens* genome then in that case you can extract unmapped reads and denovo assemble ...
written 8 weeks ago by toralmanvar900
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Comment: C: What organism's genome should be used in FastQ Screen
... I agree with andres. Still if you want to check contamination better consider model plant, fungal and bacteria genomes. ...
written 8 weeks ago by toralmanvar900
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Answer: A: How to arrange column one below another from side by side in a matrix?
... Assuming you have tsv file. This should work for file with no header in all columns: awk 'BEGIN {ORS=""} { for (i=1; i<=NF ; i++) {my_dict[i]=my_dict[i]$i"\n"}} END { for (k in my_dict) {print my_dict[k]}}' matrix.txt However, if there is header in all columns and you want to skip it then ...
written 8 weeks ago by toralmanvar900

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Scholar 7 weeks ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: How to extract specific rows based on row number from a file
Scholar 2.0 years ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
Scholar 2.2 years ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
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Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How to extract specific rows based on row number from a file
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Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to extract specific rows based on row number from a file
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