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titleclick here to see the code and output
Code Block
languagebash
titlesolution code
module load bedtools
bedtools bamtofastq -i yeast_pairedend_sort.mapped.q1.bam -fq yeast_pairedend_sort.mapped.q1.fastq #takes 1-2 minutes
more yeast_pairedend_sort.mapped.q1.fastq

Here is an example of two sequences (and their corresponding quality scores):

 

Code Block
languagebash
titletwo lines of a fastq file
@HWI-ST1097:127:C0W5VACXX:5:2212:10568:79659
TACCCTCCAATTACCCATATCCAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATACTGTTCTTCTACCCACCATAT
+
CCCFFFFFHHHHHJJJJJIIJJJJIJJIJJIJJIIIIJJJIJJIJJIJJIJJJJJJJJJJIIGGIGEGAEHFEFFEFFFDEEE@CCEDCDDD>ACBBDCA@
@HWI-ST1097:127:C0W5VACXX:5:2115:19940:13862
TAGGGTAAGTTTGAGATGGTATATACCCTACCATCCACCATGACCTACTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAA
+
?B@DF2ADHFHHFHJIIIGCIHIGGIJJJJGHIIIGIJEHHIGGGAHEGGFGHIECGIJIIIJIIIIIJJJJJJE>EHDHEEEBCDD?CDDBDDDDDDCDB

As we discussed earlier, the top line is the identifier for the sequence produced, the second line defines which bases were produced, the third line indicates the strand the sequence is aligned to, and the fourth line indicates the ASCII based quality scores for each character in the second line.

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Expand
titleclick to see the code and output
Code Block
languagebash
titlesolution code
module load bedtools #if you haven't loaded it in for this session
bedtools bamtobed -i yeast_pairedend_sort.mapped.q1.bam > yeast_pairedend_sort.mapped.q1.bed

more yeast_pairedend_sort.mapped.q1.bed #to examine the bed file visually
wc -l yeast_pairedend_sort.mapped.q1.bed #to get the number of lines in a file

use ctrl+c to quit more

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