Dear all,
Initially, I had 4 .fastq file, L001-L004, obtained from NGS of a mixture of RNAs. After several processes, I got 4 corresponding sorted bam files. Now, I want to obtain a text file that show the starting position of reads in reference sequences. However, by using
for i in *.sorted.bam; do bedtools genomecov -d -5 -ibam $i > $i.txt; done
I was only able to obtain 4 seperate txt file. Moreover, starting positions that have no reads were also included. Here is your reference when position 2, 4, 7, 10 were included:
Pri-let-7e 1 3
Pri-let-7e 2 0
Pri-let-7e 3 1
Pri-let-7e 4 0
Pri-let-7e 5 1
Pri-let-7e 6 2
Pri-let-7e 7 0
Pri-let-7e 8 1
Pri-let-7e 9 1
Pri-let-7e 10 0
Pri-let-7e 11 1
Pri-let-7e 12 3
So, is there any way that I can take to get ONE txt file reporting the starting positions with read counts from 4 sorted bam files and obmitting that with 0 count? Thank you all!
Hi, try this:
for i in $(ls *.sorted.bam); do bedtools genomecov -d -5 -ibam $i | awk '$NF > 0' >> all.txt; done;
If you want delimiters in the all.txt file you can add:
for i in $(ls *.sorted.bam); do echo "#"$i >> all.txt; bedtools genomecov -d -5 -ibam $i | awk '$NF > 0' >> all.txt; done;
edited1: double quotes to single quotes in awk.
edited2: description
1)
- for i in $(ls *.sorted.bam): For all files ended with ".sorted.bam";
- do bedtools genomecov -d -5 -ibam $i : Execute the bedtools task;
- | (pipe): send the out of the previous to the next command;
- awk '$NF > 0' : print (echo) only lines that have the last ($NF) column value greater than 0;
- >>: append output to file "all.txt".
2) echo "#"$i >> all: add "#"+"name of the origin file" to "all.txt" before the bedtools output.
Hi Hugo Leonardo de Ávila
Thank you for your valued help.
However, could you show me the difference between two outputs of the two commands that you suggested?
Thank you!
Off course,
The first one is going to output a file ("all.txt") like this:
Pri-let-Xe X X
Pri-let-Ye Y Y
Pri-let-Ze Z Z
....
Te second one will output the names of the origin files as a delimiter in case you want to split the result file "all.txt":
#File1.sorted.bam
Pri-let-Xe X X
Pri-let-Xe X X
Pri-let-Xe X X
...
#File2.sorted.bam
Pri-let-Ye Y Y
Pri-let-Ye Y Y
Pri-let-Ye Y Y
...
#File3.sorted.bam
Pri-let-Ze Z Z
Pri-let-Ze Z Z
Pri-let-Ze Z Z
...
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