Question: Weird output when trying to convert sam to bam!
0
gravatar for Parham
4.6 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

Hi,

I have mapped my reads using STAR. Then I am trying to convert the output SAM file to BAM using code below but I get a strange respond. Could somebody tell what I am doing wrong? Thanks in advance. 

samtools view -Sb Aligned.out.sam aligned.bam
[samopen] SAM header is present: 6 sequences.
�BC}͑�N�@��jL�S��ca�
[main_samview] random alignment retrieval only works for indexed BAM files.
��Zc<y2��|�ͷ;3��9=y�0�M8{d���q3���6I��H!鈳CDvF�S��hX��<��ۚԚJT����e��y��+�i�."��܀U�fI4�
                                                                                            ^[����*�D����bQ�Pe�8��jR�i��6�Z��VTD!I#���*�R_&CKru˴
�I���`]���1E���9���i>���<��m                     ѧI���!D��+$%1f�B�x�0.�Ӳzd�p���g�e�2؏=t�
                               �Y����^�:�5�l�0�6��N���[�    ��F���BC%                 
sam samtools bam • 1.7k views
ADD COMMENTlink modified 4.6 years ago by Pierre Lindenbaum123k • written 4.6 years ago by Parham1.4k
1
gravatar for Pierre Lindenbaum
4.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:
you need to specify the output '-o (out.bam) ' argument

samtools view -Sb -o aligned.bam Aligned.out.sam

 

ADD COMMENTlink written 4.6 years ago by Pierre Lindenbaum123k

Oops, sure I need to. Thanks a lot! 

ADD REPLYlink written 4.6 years ago by Parham1.4k
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