How to convert mapping bam file to fastq without loseing the mapping information
I want to create my RNA mapping data into a library for further analysis. Now I have bowtie2 mapping data, which is in bam files, I now use bedtools to extract fastq mapping reads from those bam mapping files. (bedtools bamtofastq function) But it seems like the fastq data produced by bedtools would only contain the original sequence name, but not which , for example , chromosomes it mapped to, and where it is.
Below is my bam files, I want to have the the mapped chromosomes and location information in the name of the fastq files, what I could do? Is there a simple way to do it? I have tried to do the replace with ‘sed’ command, but not very successful so far. Below I attached my bam files info and my attempt to replace names with sed command
while read p; do echo "$p"; sed -i -e $p mapped.fastq; done < replacename.txt
replacename.txtin each line, is in
my bam files that need to convert to fastq
SRR1761528.1829103 16 CL1Contig15_2_sc_0.515159_l_155 337 1 50M * 0 0 TTGGAGTGTATTGGGTGCGTTCGTGGCAAAAAATCACTTCGTGATTCGCG BFHFEECHEIIIHDIIIIHDIIIIIHDHIHIIHEG;GFHFHHDD<FF@@@ AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:32C17 YT:Z:UU SRR1761528.942684 16 CL34Contig23_2_sc_0.402716_l_155 34 0 12M1D38M * 0 0 TTTGGACATATTGAATTTACTGGGTGCGTTCGTGGCAAAAACTCACTTCG JJJJJJJJJJJJIJJJJJIJJJJJJJJIJJJJJJJJJHGHFHEFDFFCCB AS:i:-26 XS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:12^G2G1G2T30 YT:Z:UU
For example, I want the
CL1Conitg15_2_sc_0.515159_l_155 to be included in the fastq sequence name, to form like
If anyone has a good idea?
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