Hi,
I am new to Bioinformatics and I am trying to use the samtools view command. I have generated the SAM file but the header is missing so I followed this link (http://davetang.org/wiki/tiki-index.php?page=SAMTools) and tried the commands, but I get the following error -
samtools view -bS new_test.sam > new_test.bam
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
cbil@cbil-desktop:~/bowtie-linux/bowtie-1.0.1$ samtools view -bT e_coli_1000.fa new_test.sam > new_test.bam
[samfaipath] fail to read file e_coli_1000.fa.
[main_samview] fail to open "new_test.sam" for reading.
Can someone please help me?
Thanks!
I am new to Bioinformatics and I am trying to use the samtools view command. I have generated the SAM file but the header is missing so I followed this link (http://davetang.org/wiki/tiki-index.php?page=SAMTools) and tried the commands, but I get the following error -
samtools view -bS new_test.sam > new_test.bam
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
cbil@cbil-desktop:~/bowtie-linux/bowtie-1.0.1$ samtools view -bT e_coli_1000.fa new_test.sam > new_test.bam
[samfaipath] fail to read file e_coli_1000.fa.
[main_samview] fail to open "new_test.sam" for reading.
Can someone please help me?
Thanks!
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