sam to bam conversion

Question

[sa1987]

hi

i m working on rna seq analysis in human

i got my sam file

@HD VN:1.0  SO:unsorted
@SQ SN:NC_000001.11 LN:248956422
@SQ SN:NT_187361.1  LN:175055
@SQ SN:NT_187362.1  LN:32032
@SQ SN:NT_187363.1  LN:127682
@SQ SN:NT_187364.1  LN:66860
@SQ SN:NT_187365.1  LN:40176
@SQ SN:NT_187366.1  LN:42210
@SQ SN:NT_187367.1  LN:176043
@SQ SN:NT_187368.1  LN:40745

my tired converting to BAM result file looks like this

BAM
U�:^@HD VN:1.0  SO:unsorted
@SQ SN:NC_000001.11 LN:248956422
@SQ SN:NT_187361.1  LN:175055
@SQ SN:NT_187362.1  LN:32032
@SQ SN:NT_187363.1  LN:127682
@SQ SN:NT_187364.1  LN:66860
@SQ SN:NT_187365.1  LN:40176
@SQ SN:NT_187366.1  LN:42210
@SQ SN:NT_187367.1  LN:176043
@SQ SN:NT_187368.1  LN:40745

my bam file siz is more than 5 gb

i want to sort it but when i try sorting i get this error

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).

Segmentation fault (core dumped)

plz help

shafna

[Pierre Lindenbaum]

result file looks like this

it's a binary file, you shouldn't open it with more or another text viewer

i want to sort it but when i try sorting i get this error

show us the full command lines.

[sa1987]

this is the command i used samtools sort humangenome_1.bam humangenome_1_sorted

my samtools version is 0.1.19

[Matteo Schiavinato]

You probably converted without adding the -h option that keeps the header. The full conversion command is:

samtools view -b -h input.sam > output.bam

[brent_wilson]

You have to be careful with pipes and redirects when converting between SAM and BAM. Don't clip off anything (such as the header) that may be needed for a complete file.

Brent Wilson, PhD | Project Scientist | Cofactor Genomics 4044 Clayton Ave. | St. Louis, MO 63110 | tel. [phone] Catch the latest from Cofactor on our blog.

[h.mon]

Which version of samtools?

[sa1987]

samtool 0.1.19..its a older version ...i also ahave another question how to update the samtools 1.4?..i tired "sudo apt-get install samtools 1.4"--> but i am getting error

Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:

The following packages have unmet dependencies: libstarpu-1.1-4 : Conflicts: libstarpu-contrib-1.1-4 but 1.1.0+dfsg-2ubuntu1 is to be installed libstarpu-contrib-1.1-4 : Conflicts: libstarpu-1.1-4

after this i tired checking the version ...its the same old version..

plz help

Answer 1

[shmaisrael]

If you use samtools 1.3 you can do it with next command

samtools sort -n -o out.bam in.sam