I am trying to analyse some old data on STAT3 binding locations in macrophages upon IL-10 treatment. I found a dataset which perfectly matches what I want, however it was only available in bowtie format. My initial aim is to view it in the UCSC genome browser and quickly check for peaks at my genes of interest then move on to a more detailed analysis.
I managed (with some difficulty, I'm very new to all this) to convert it into a SAM file, however when I try to upload it to UCSC I get an error. After spending a while trying to figure out what was up, I discovered that it's missing the @SEQ header.
Now, I know that it has been mapped to mm9 as the reference genome, so I was hoping someone could help me generate a basic header.
I have read around and attempted converting it to a bam, using a fasta file of mm9 chr1, however I'm kicked back given an error:
samtools view -bT Documents/chr2.fa Documents/ChIP/STAT3.txt > STAT3.bam [samfaipath] build FASTA index... [W::sam_parse1] urecognized reference name; treated as unmapped [W::sam_read1] Parse error at line 1 [main_samview] truncated file.
I would appreciate any help people can provide, or alternate methods of generating the @SEQ header, and please explain in detail, I'm new to all this and it takes me a while to understand what exactly I have to do.