User: bobbyle0210

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bobbyle021010
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9 months, 4 weeks ago
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Posts by bobbyle0210

<prev • 11 results • page 1 of 2 • next >
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Why the proportion of reads with adapters in NGS is low?
... Dear all, ---------- Currently, I am processing a NGS data using cutadapt to remove 3p and 5p adapter sequences from reads. Normally, as I notice, the percentage of trimmed reads (reads with removed adapters) could reach 95 - 99 %. But for this data, some of my sample only contain 20 - 25 % read ...
ngs rna-seq written 6 months ago by bobbyle021010 • updated 6 months ago by ATpoint36k
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Comment: C: Compare specific parts of two columns in a text file in Linux
... Hi, Thank you for your help. Could you explain in detail how the command works? I am not so familiar with linux command. Thank you :) ...
written 7 months ago by bobbyle021010
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Compare specific parts of two columns in a text file in Linux
... I have a text file with several columns separated by tab character as below: 1 ATGCCCAGA AS:i:10 XS:i:10 2 ATGCTTGA AS:i:10 XS:i:5 3 ATGGGGGA AS:i:10 XS:i:1 4 ATCCCCGA AS:i:20 XS:i:20 I now want to compare the last two columns AS:i:(n1) and XS:i:( ...
aligning_score alignment samfile linux written 7 months ago by bobbyle021010 • updated 7 months ago by bioinformatics2020140
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Comment: C: Couting number of similar reads in sam file and output in bed file?
... Hi, I notice that for my bed file (which contains ~30 million reads and ~ 2.5 GB in size), I need to sort my file using sort myfile.bed before using uniq -c. Otherwise uniq -c only will not provide expected result. What could be the reason for that? When will I need to sort my file? Thanks. ...
written 8 months ago by bobbyle021010
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Comment: C: Couting number of similar reads in sam file and output in bed file?
... That's so cool, thank you. However, if I want the output in order like this: ---------- var_1 0 15 ATGCATGCATGCCGTA 3 ---------- var_2 5 20 ATGCATGCGGGCCCC 1 ---------- Is there any command that I can use? Thanks. ...
written 8 months ago by bobbyle021010
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Couting number of similar reads in sam file and output in bed file?
... Hi all, Currently, after mapping, I got a sam file which contained approximately 30 million mapped reads. Then, by using bedtool bamtobed, I was able to obtain a bed file. However, there were so many many similar reads. Therefore, in order to reduce the size of the final bed file, is there any way t ...
bedtools samtools rna-seq written 8 months ago by bobbyle021010 • updated 8 months ago by Carlo Yague5.0k
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Counting starting and ending positions of reads in reference genome
... Hi, Currently, I am working with NGS processing data. After getting SAM/BAM file, now, I want to output a text file that indicates the starting (5 end) and ending (3 end) position of each read in the corresponding reference sequence as well as the sequence of the read. The output file may look like: ...
bedtools ngs bam sam rna-seq written 9 months ago by bobbyle021010 • updated 9 months ago by Pierre Lindenbaum129k
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Comment: C: Error when installing bedtools
... Hi, thank you for your suggestion. But after this 2 steps, I still cannot run bedtools. It showed "command not found". What can I do now? ...
written 9 months ago by bobbyle021010
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Comment: C: Error when installing bedtools
... Hi, Could you show more detailed steps for this, because I am not familar with linux yet? Should I follow this guideline: ---------- $ wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz ---------- $ tar -zxvf bedtools-2.28.0.tar.gz ---------- $ cd be ...
written 9 months ago by bobbyle021010
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Comment: C: Error when installing bedtools
... I cannot find the source to download gcc/g++. All guideline on the internet shows the use of sudo command. Could you give me some reference? ...
written 9 months ago by bobbyle021010

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