Hi
I'm trying to perform snp calling of a fish species but itś being a hard
task. My current problem is the following:
After indexing a reference genome (bowtie2-build), align my sequences to
this genome (bowtie2 -x) and converting SAM to BAM (samtools view -bS) I'm
unable to perform samtools sort command. Result is a weird buch of symbols
followed by letters and numbers as follows (just a part of it):
yOR�����G(��< {`�m�wF�D/�q|lOS�}�HӁ 7P ����]��)G��x=LǗ�� #<\�v����[�
���\��n�O~'�mZ ��D3�pq�}�Ʀ����`�w���_�? ��K���%��1eEF[3Gy�)� �_w$�(��L+���
�� �� ��f�D���%iu4�H��Y�rfH���pe:�v W�/�2, '�I�� � <8o��� �su��Z�������
{����r� �b ����)F}�N5 {4O��ւ���b���o������e W8�X9�
�DO��� � d5�t(F C;4 E�p���XcαW^��(Nr ���g�������$�D�� � e��� � BC
phcarvalho@mapinguary
:/hiseq2019/katpel_refmap/t;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;c62;
I realized that my SAM files when inspected using 'head' command display
the same symbols. This makes me wonder if the problem is not with the SAM
file. Maybe the problem concern one of the previous steps that I have
mentioned above. So, I briefly describe the results of these three previous
steps below:1.bowtie2-build $ sudo /opt/bowtie2/bowtie2-build /hiseq2019/katpel_refmap/thualb/GCA_900302625.1_ASM90030262v1_genomic.fna /hiseq2019/katpel_refmap/thualb/thualb (four pages of calculation) Total time for backward call to driver() for mirror index: 00:19:01 2.bowtie2 -x $ sudo /opt/bowtie2/bowtie2 -x /hiseq2019/katpel_refmap/thualb/thualb -U /hiseq2019/katpel_refmap/teste_trimming/Kp02.R1headcrop.fastq -S Kp02.sam --no-unal -p31 3006792 reads; of these: 3006792 (100.00%) were unpaired; of these: 1266671 (42.13%) aligned 0 times 1398982 (46.53%) aligned exactly 1 time 341139 (11.35%) aligned >1 times 57.87% overall alignment rate 3.samtools view $ samtools view -bS Kp02.sam > Kp02.bam [samopen] SAM header is present: 38995 sequences. Also, the result of SAM is weird as it does not seem to fit the usual file format: $ head Kp02.sam @HD VN:1.0 SO:unsorted @SQ SN:OMLG01000001.1 LN:1427 @SQ SN:OMLG01000002.1 LN:12368 @SQ SN:OMLG01000003.1 LN:56682 @SQ SN:OMLG01000004.1 LN:34652 @SQ SN:OMLG01000005.1 LN:30301 @SQ SN:OMLG01000006.1 LN:2594 @SQ SN:OMLG01000007.1 LN:14873 @SQ SN:OMLG01000008.1 LN:13482 @SQ SN:OMLG01000009.1 LN:10753 The command used to perform samtools sort was samtools sort -O bam -o Kp03_sorted.bam Could anyone bring me some light? I'm new to bioinformatics and have been struggling to learn it by myself. Thanks! Professor Adjunto ------------------ *Instituto de Biodiversidade e Sustentabilidade* *NUPEM - UFRJ* *Universidade Federal do Rio de Janeiro* Av. São José do Barreto, 764 São José do Barreto, Macaé, RJ CEP 27965-045 ------------------ «Be Yourself. Everyone Else is Already Taken.»
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